It wouldn't surprise me if Gregory had molested Rachel. In fact, I think he still wanted her as an adult when he is reunited with her at Collinwood and browbeats her into returning to Worthington Hall.
In some ways I think he is responsible for what happens to Rachel in the end.
SPOILER ALERT:
If he hadn't had Evan Hanley brainwash Tim Shaw into killing Minerva, Rachel wouldn't have had to hide him in that farmhouse, she never would have been bitten by Dirk, and she would never have been shot by Judith.