I'm not sure how college fans are affected, not because there isn't an overlap between the two groups of fans, but because the fandom is separate. In fact, fans of college programs with players in the W might follow and root for a team that includes players from their school, or they might just root for a local team. My wife and I root for both the Liberty (because we had season tix back in the day) and for the Mercury because they are (relatively) local. I root for the members of the 2 teams because they are on the team, regardless of where they went to college. But I don't see why this would affect my opinion of rival teams where these WNBA players no longer are.
As to the players, rarely have fan rivalries extended to individual players. A Rutgers player, for instance, might have wanted to beat the UConn team in the worst way, but that doesn't mean that the player disliked the players she was competing against. And yes, good natured ribbing in the locker room probably does go on.