The first argument is that the issues of hard sciences can be bracketed off from the prevailing thrust of the standpoint theory critique. I actually heard this argument best phrased in a critique of certain post-modern legal theorists, but it struck me as a solid formulation. Standpoint theory can be applied to simple isolated descriptive cases. The sentence "the top of Mount Everest is snowy", for example, could raise questions about when a hill becomes a mountain, when the middle becomes the top, and why the referenced mountain is signified by the Western notation of "Everest" rather than an indigenous name. Nonetheless, this is not what most post-modernists do with their time. The topic of snow on Mount Everest is relatively uninteresting to us. By and large we are talking about social phenomena--political organization, distribution of resources, societal structures--areas in which the criticism is much stronger. So if the kernel of hard science is indeed not contingent on standpoint, that doesn't take out much of the theory's most fertile ground.
But even still, I think that standpoint does influence science writ proper on the front and back ends of the process. The front end, because standpoint directs what sorts of research questions are "interesting", which projects get funding, what Ph.D. programs train their disciples to do, etc.. For example, it is only recently (I mean really recently--within the past dozen years) that there has been any research on the basic anatomy and function of the clitoris. Most biologists are male, their attention was (ironically enough) elsewhere, and so the subject was completely neglected for years. We don't have time to research everything, and how we use our precious time is mediated by the gatekeepers to the scientific profession who can make the labs and the equipment and the funding available.
Science is also influenced by standpoint on the back end, because at the point where science leaves the laboratory and enters the real world to have a social impact as a policy or philosophy, those impacts and interpretations are also socially conditioned. A study which shows that we could create a completely clean-burning, renewable resource that would satisfy all our energy needs, but it would require some massive expenditure of resources from the First World that would sacrifice their economic advantage can "mean" that it's possible if we're willing to demand heavy sacrifices, or it can "mean" that it's cost prohibitive and infeasible, depending on who gets to determine meaning. More directly, scientific disciplines that see themselves as having insights on human nature or behavior are particularly prone to be usurped by the dominant classes to reify their position and dominance. The argument simply is that people who are on top of unjust hierarchies will grasp at any ammunition that buttresses their stance, and science can often be utilized towards these ends. Since the dominant classes control the means of (knowledge) production, it is difficult for alternative views or interpretations to surface.
Finally, there has been interesting research on how science itself constitutes a "mentality" or standpoint that is not neutral but can lead to very specific ideological outcomes. George Kren & Leon Rappaport used the Holocaust as their example, giving three problems with the scientific mentality:
[T]he prevalent view is that science is neutral, a method of gaining knowledge leading to control over the physical and social environment, and evil only insofar as evil people may use it badly.
Our view is different....Quite apart from the technology, the mentality of modern science is what made the Holocaust.
[First]....the...central role of science as a mentality was in providing the inspiration and justification for these technical activities. The abstract, categorical thinking encouraged by the culture of science paves the way for acceptance of categorical racist ideas.
....Once it is accepted that such abstractions as genes distributed in populations are, so to speak, ‘real facts’ instead of theoretical constructs, the way is opened toward instituting and justifying social policies based on these ‘facts.’
The point at issue here has nothing to do with whether or not there is can be some merit or utility in the accumulation of evidence leading to scientific generalizations about people; it is that in a scientifically oriented culture, people will accept generalities produced by science as fact, particularly when the generalities fit other culturally determined predispositions or biases.
[Second,] [t]he scientific orientation in Western civilization also encourages and even forces people to detach their emotions from the rational intellect....This is not to say that ignorant, brutish people with no education and no ability to detach emotions from intellect are not capable of performing horrible actions....But...designing an efficient system of death camps.... is only possible as a manifestation of detached technical expertise grounded on a scientific rationale or logos, and only in a relatively small degree supported by emotionality or passion.
It should be clear that the mental splitting which separates emotionality from rationality is deliberately inculcated by science-oriented Western culture in order that people may repress or suspend reflexive emotions that might block achievement of abstract, distant goals. The ability to categorize objects, to then perform mental (imaginary) operations upon these objects, and thus transform the meaning of the objects into something other than what one started with is fundamental to all science.....By exercising this capacity, we can make judgments that some people are better than others, and, ultimately, that some people are not even people at all. So it is that the scientific mode of thinking—the mode of thinking required and promulgated by science—allows us to perform promethean acts that transform the world.
[Third,] science....is irrelevant to questions of morality or value, which stand at the center of the human condition. Science appears, consequently, as hardly more than a wonderfully complex and plastic plaything of the intellect, a toy that can be shaped in whatever forms clever intellects wish to shape it. It follows that science is totally amoral and terribly dangerous because its potent effects are ungoverned by any intrinsic human limits. We see it ever more clearly these days, of course: the weapons, nuclear plants, food additives, pollutants, etc., that cumulatively, as the result of science, threaten the future existence of our species and determine the conditions under which we exist. [George Kren & Leon Rappaport, “The Holocaust and the Human Condition” Thinking the Unthinkable: Meanings of the Holocaust, Roger S. Gottlieb, ed. (Mahwah, NJ: Paulist Press, 1990): 347-72, pp. 357-361]
Orthodox Rabbi Irving Greenberg made a very similar point in his famous essay, "Cloud of Smoke, Pillar of Fire,":
In so many ways, the Holocaust is the direct fruit and will of this [scientific modernist] alternative. Modernity fostered the excessive rationalism and utilitarian relations which created the need for and susceptibility to totalitarian mass movements and the surrender of moral judgment. The secular city sustained the emphasis on value-free sciences and objectivity, which created unparalleled power but weakened moral limits. (Surely it is no accident that so many members of the Einsatzgruppen were professionals.) Mass communication and universalization of values weakened resistance to centralized power, and served as a cover to deny the unique danger posted to particular, i.e. Jewish, existence. [Irving Greenberg, “Cloud of Smoke, Pillar of Fire,” Holocaust: Religious and Philosophical Implications, John K. Roth and Michael Berenbaum, eds. (New York: Paragon House, 1989): 305-48, pp. 320]
The upshot isn't to say we should revolt and overthrow the Biology department (though I've been known to advocate that, it is strictly a result of academic, not philosophical, frustration). The point is that we should not exalt science as existing on a plane beyond society, beyond social implications, beyond the people who build it and beyond the people who apply. Science may have an independent reality, but insofar as its reality intersects ours it matters who controls the relationship between it and us. That, beyond all else, is why standpoint theory still matters for scientific relationships.