First, the show isn't the show to have a large sustained cast. Its a dangerous world and the characters have a high death rate. But they have still created several female characters that worked. Some were intended to be one offs, some were used and killed to show the nature of the business and some weren't available for work when the writers wanted to use the characters (the reason Missouri wasn't a regular, and why Ellen wasn't used in season three).
As for the producers writing out Jo do to fan reaction, I think thats highly unlikely. As by the time the fans got to see Jo, the writers we already working past the point Jo was basically written off.
It took very little time (after seeing dailies and final edits) for the producers to see that certain aspects of what they created weren't working. That includes the Roadhouse, the psychic kids (meant to consume far more time and last much longer).
As for Jo herself, I just didn't buy the actress in the role, until Born Under a Bad Sign. From the point to the her last appearance I have nothing but positives to say about the character. And the character always maintained her attraction to Dean.
As for SPN's audience. It has long been stated by many, many people to have a larger female fan base. That really isn't accurate. It has a vocal female fan base, but they aren't the majority of the shows audience.
Which in and of itself is rather odd, as almost all scripted network shows have a larger female audience (women watch more non sports then men). But SPN through its run on the CW (and even later with DVR results) has a statistically even breakdown 50.6% male/ 49.4% female.
Even when it aired after VD where its same day audience was significantly female its DVR audience balanced it out and was primarily male.
And the show did absolutely indeed to keep using Ellen after season two, but with the studio mandated introduction of Bela, the writers strike, and the actress being unavailable during the times the writers were interested in using her, killed it. By the time season 4 came about, enough time and having much more focused stories with specific cast needs (less hunters for example), keep her off the show.