OP - I honestly don't know about Mary. I don't like it when she's completely villanised, but I also don't think her actions are excusable. I think Sherlock trusts her not to hurt John, and I don't want him to be wrong about that. I don't think Mary is completely heartless and in my headcanon she really wants to be the person she presents herself as in TEH and TSoT, but she's not able to do it. She loves John in her way, so Sherlock trusts her as far as John is concerned, but not really in any other respect. I don't think he would encourage John to stay with her if he thought there was the tiniest possibility she could hurt him.

Did that make any sense? In any case, you don't have to stick to it. Write what works for you, I'll be happy for any kind of fill!