On the what of it is not Thomas, but a shape shifter; I don't think it is the case, but if it is that person is really hardcore. Facing being imprisoned forever and not flinching takes a lot of nerve.
Also, I think Jim said once that Grey could probably become Harry to a degree that he could use some or all of his wizard powers, bit that the transformation would be so complete that Grey would effectively be gone forever. Of course only Lara knows if that is the case, since she fed him and could have faked that. Then the charge would be to uphold the illusion.
With that being said, I don't think it is odd that she charges him. It seems a fair amount of people on the forums reasons that if you get to a certain position of power and responsibility all your actions will be well reasoned out and emotions will never affect that reasoning. So far the only ones in the series who seems to live up to that inhuman ideal are (suprise) the ones that are not human in any way. I guess the angels are the best, maybe only, example.