Well, I think the clues are a red herring .... only time will tell I suppose.
Branson's socialism is moderating, at least, in no small part due to his interaction with his in laws.
As for Thomas being a "bad guy", you may have a point. On the other hand, is his bad character implied to be the result of the intolerance shown to homosexuals at the time? In that case we have a very subtle justification taking place.
Note also his rehabilitation was written into the script by making him play the hero and take a beating to spare Jimmy.
In any event given his defects of character and homosexuality I strongly doubt any family at the time would have taken him back, especially after having gotten him so successfully out of the way. One would think that they would be thanking their lucky stars ... and to have Bates as the instrument of his return defies common sense.
My two cents anyways ...