I think if you want to complain about Molly's and Sally's treatment, it's more on the writers than the fandom really. From the very little canon we have, Sally is portrayed as bigoted (i.e. always referring to Sherlock as 'Freak' and 'Psychopath' which, I'll be honest, bothers the hell out of me) and she's fairly seriously slut-shamed. Molly is shown as desperate. I just don't think that the way the characters are written allows for a very positive view of them.

Also, most of the fanfic I've read puts Sally, at least, in a much better light.

I'm not saying that the only reasons that people dislike Sally and Molly are down to the writers, and I'm sure there are people who do dislike them for the reasons you mentioned, but I haven't seen much evidence for what you're saying in the fandom.