It might. For instance Stephen J. Gould, an evolutionist who happened to be an atheist, famously argued that even major trends in evolution were almost entirely a matter of chance, so that if you went back a couple billion years when there was only bacteria, and started the whole process again, you'd get two billion years later a biological world that was radically different from the present one. You wouldn't get anything like humans, nothing identifiable as "mammals" or "reptiles," maybe you would get intelligent creatures but maybe you wouldn't, maybe you wouldn't even get "animals" at all.
OTOH a equally important (and even more accomplished) evolutionist, Simon Conway Morris, who happens to be a devout Christian, argues almost the opposite, that there is a "recurrent tendency of biological organization to arrive at the same 'solution' to a particular 'need'," and that if you reran the broad experiment of evolution you probably would get something broadly similar to what we now have.
Is there some relation between these differing conclusions and these men's differing philosophical views? Probably there is. But so what? In science the origin of an idea is irrelevant. All that matters is how well the idea works. If general relativity had come to Einstein in a dream it's validity wouldn't suffer one whit.
Individual scientists aren't required to be "neutral". They can be as opinionated as they want. They can be motivated however they want (or however they are). But their ideas have to compete on their merits. For instance I always thought that Robert Baker -- a dinosaur paleontologist who famously argued starting back in the 80's that dinosaurs were warm blooded, and that birds evolved from dinosaurs and not from pre-dinosaur thecodonts -- was arrogant, bigoted, and responded poorly and unfairly to criticisms of his ideas. So what? His ideas were criticized never-the-less because other scientists are also opinionated but hold different opinions. And Baker's ideas have (so far) prevailed. It's not Baker's personality, nor the "philosophical underpinnings attendant to [him as an] observer," that determine the validity of his ideas. It's the ideas themselves, and how well they actually work (or fail to) that matters.
Do you think the federal government should dictate which philosophical underpinning should govern science?
No, I don't think it should. I also don't think it HAS. For instance that Intelligent Design is not genuinely (at least yet) a part of science, and that it's attempted promotion by the school board in Dover had a transparently religious motivation, is nothing but (a remarkably well established) observation and recognition of fact.
You're stewing over the (purported) extra-scientific implications of evolution or ID, and implicitly claiming that they are what matter. But they don't mean spit, not as to the scientific standing of either idea. Let's say that ID actually does succeed as science at some future time. Would there be ANY validity to criticisms that it was improper (even to a degree) to teach it in science classes because it was "theistic"? Of course not. Would there be ANY validity (again even to a degree) to arguing that it should be "balanced" by some "atheistic" or "non-theistic" idea? Or course not. It should only be balanced to the degree, and only to the degree (including to no degree), that some alternative idea also maintained objective scientific standing.
And that is why the presence of organized matter that behaves according to laws, when attributed to an intelligent agent, is not a wholly wild, or untenable, or unscientific idea. Nor is the idea that an intelligent designer does not always attend directly to the product he/she/it designs. Nor is the idea that evidence of a person or phenomenon can be indirect.
I don't know what Behe et al are trying to do with this intelligent design schtick. If they are attempting to replace atheistic science they are wrong-headed. Atheistic science is somewhat reasonable and deserves a hearing in the academic marketplace. If they are attempting to demonstrate that intelligent design is a reasonable way of viewing the universe either inductively or deductively, well, DUH!