One of the big themes in Peace Talks is misdirection or misunderstandings.
I agree with this, and there's definitely something iffy here.
But I don't think having someone else beat up Thomas solves the problem. He ought to have healed from a beating by a Genoskwa or Naagloshii, too (sure, those beings could kill him, but short of death his healing powers should still work barring a token of True Love, and those creatures won't have that).
The more I think about this, the more I lean toward the idea that "Thomas" isn't actually Thomas, and he's conveniently too beat up to talk so Harry and Lara can't tell that he doesn't have Thomas's personality or knowledge.
But I'm not sure that works, because he was able to take energy from Lara, and Alfred ought to have known what he was imprisoning.
...Though that makes a lot of assumptions. There are lots of things that feed on energy. Alfred might not
care, and all he really says is that 'Thomas' isn't really powerful enough to deserve minimum security.