You don't really lose that much fans to be honest. I just chose my friend over the big time agent and my popularity dropped a bit but then the next two games or so, it shot back up.
Two things happened that made it shoot back up: I was subbed in at the last 6 seconds of the 4th quarter and the coach told me to make the game winning shot, I did and we won the game. Second thing that happened that made my popularity shoot up was there was this BS rumor that I was isolating myself from the team and that I would eat lunch in my car instead of with the team. The reporters asked if it was true, and I responded that it had no truth to it and I gained more fans again. I also just got the Prime Time personality badge and you get that by having like 2+ million fans. Team Chemistry is around 83% and Local Fans around 81%. So yes, choosing your friend has some drawbacks but you recover quickly if you play well the next 2-4 games after.