I've never made any of the NPC violent with me. So I don't know with certainty and Thomas being of unique importance. It is hard to know, but my guess would be that it'll all be there still. NG+ does revert the state of everything other than world and player tendencies (though it may revert those as well). So killed NPCs will be back. He'll definitely be there.

Usually unless you attack repeatedly or do a lot of damage in one hit, the NPCs will forgive, though being annoyed by a mistake. It is still very nerve racking though always fearing that you may accidentally hit an NPC.