Perhaps not direclty but possibly Fanny does cry at times becuase unconsciously she hopes for sympathy from Edmund... He is the only one who shows her any and he's sometimes dense and clueless, but he's not immune to tears...
I dont see him as malicious at all... He's a nice guy but often stupid and insensitive. I dont blame him for not falling in love iwth Fanny or not even noticing that she has feeligns for him, but I do agree that he's a bit less than sensitive in his trying ot make her reconciled to Mrs Norris' house.. He must know waht Mrs N is like really. If he doesn't... and to try and persuade Fanny that she'll be OK there doesn't seem to me to be very kind. Possibly it is no more than his knowing that he would be unlikely to be able to change things, ie if mrs N really wnated F to live with her.. Edmund would not have any real say in it.. but he could IMO at least try....