I agree with you her friendship with Fanny is mostly insincere. If it were sincere she would still be sending Fanny letters all along.

I must give her the credit for this in Ch. 30 though.
“Henry, I think so highly of Fanny Price, that if I could suppose the next Mrs. Crawford would have half the reason which my poor ill–used aunt had to abhor the very name, I would prevent the marriage, if possible;"

At least Mary would not wish that on Fanny. I agree though, their friendship was mostly of convenience. When she was speaking of Fanny as a sister should, I bet she was speaking more than she actually felt. I doubt that with Maria she was bad mouthing Fanny. I think with time and distance, she would definitely bad mouth Fanny as she did her other friends though. It's just that at that point of the story as Henry's potential fiance, Fanny was in Mary's "circle of trust". :)

It's interesting too, Fanny doesn't truly like Mary either, but she still behaves to her as a true friend should. In that respect she is like Elinor. Though she may not like someone, she always tries to treat them with the respect she thinks they deserve.