I think they'll at least try him at the three. If he can stay with big SFs, he should be able to stick. The small-forward in the Spurs system really only needs to be able to space the floor on offense, which Thomas can do.
Really, how much different is he from Kawhi? Long, skinny combo-forwards who excel at rebounding. Kawhi is good as stealing, and Malcolm is good at blocking. Kawhi is probably a more diverse person from midrange while Thomas is looking better from distance. Not saying Thomas is as good as Leonard at all, but he is a three in the same mold.