I think your argument about "a small group of tribes acting in concert to exercise determination over one set of remains, from a group/groups attempting to impose a national religious agenda" hits the issue directly.
For Myers to say that Indians should be treated with respect, but not their superstitions, is a statement remarkable in how effectively the second clause demonstrates the insincerity of the first.
What could be more calculated to disrespect Indians than saying such a thing? (Well, other than grave-robbing.)
To be fair to Myers, he's not a fan of *any* kind of religion; it's all superstition to him.
But we don't have to be fair to Myers, by his rules our respect for him should be dictated by how similar his views are to ours, where they differ we're no longer required to show him respect. 
My point is at least there's consistency there; the problem is that the consistency *overlooks* an important point of difference, not that difference implies no need for respect. Which is why I thought that, as an argument against Myers, the point about the vast difference between the politics of religion in the Indians' case and in the case of the Religious Right was a powerful one.
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