Ideally, it would be great if I could use the petitioning / recruiting angle on PrC's that allow it. But in my campaign, I allow level-ups immediately after gaining the exp and sleeping, so 90% of the level-ups occur while the group is out adventuring, typically in the wilds or in some remote locale. It wouldn't be very easy to force them to wait until they next reached the correct location for this or that guild to gain their next level.
Thus, I just let them instantly take the class if they qualify for it. It's not perfect, but it's less hassle for everyone. Hence, the players have more fun and that's the whole point isn't it?