1) That is my point:
If Thomas was a danger, Mouse would react. Mouse did not react. Therefore, Thomas is no threat. Eb should realize that, but he is too biased.
2) Thomas was never alone with Maggie. HARRY was with them (as well as Mouse).
3) What Mira says. Also, apparently there is a comic where the wardens fight alongside Thomas. And he has been an ally of Harry for years while he was dating Luccio, for instance. There is no reason for him to believe Harry is being mind controlled for him.