I tend to discount historical conspiracy theories and take ideological writers at their word unless they are obviously propagandizing.
In general, I agree. Some Straussians go way overboard in their obsession with "secret writing." However, even in their excess they often reveal facets ignored by the standard interpretations. For instance, Locke is always said to have been a student of Hooker, the Anglican divine, when there are significant reasons(detailed by Paul Rahe) to believe that Locke creatively misquoted Hooker. Locke is also often contrasted with Hobbes, taking at face value Locke's lumping him in with "other justly decried authors." In fact, Locke works from within a state-of-nature framework that shows a strong Hobbesian influence, instead of the traditional Hooker-type natural law theory.
My point about the corporate aspects of salvation alludes to the Christian Church as the Body(corpus) of Christ. I meant it in the ecclesial sense, not in the strictly physical one. Locke's egalitarian philosophy favors a type of Christianity more compatible with "low church" pietistic congregationalism than the "high church" hierarchical and liturgical churches.
There's a million dollar question. American libertarianism is a coat of many colors. However, if we restrict the field to just those libertarians among the founders, then the answer is that Locke was an influence on libertarian thinkers of the period, but, IMO, to cast him as proto-libertarian seems to be going a little far. For example, Locke placed much more emphasis on the universality of the social contract than did our founders. The framers of the Constitution surely felt that the social contract of Philadelphia was most certainly different than that of Charleston and to attempt to mold them as one would result in tyranny.
Locke operated as a social contract theorist. The fact that adherents to that theory had a common ideological forebears with the state-of-nature theorists seems to me to be a red herring. Locke adopted the social contract stance because he felt that anything else led inevitably to government born of tyranny. He felt strongly that the governed must have some sort of formal agreement with those who govern them. To assume that Locke discards the categorical imperative because he rejects certain aspects of a natural law stance would be hyperbolic.
As for the corporate Church, being a Protestant (not an anti-Catholic), I have to say I agree with any who favor congregationalism over hierarchy and liturgy. I have no problem with Locke's stance on that, if that was his stance. I don't recall any writing by him on the subject, though. More specifically, Locke was a proponent of religious tolerance. There are several theories as to Locke's actual religious beliefs, but they will likely remain theories since he lived under a theocracy that had a nasty habit of burning dissidents.