She pretty much said, "If you're still at the party when the spell's time limit is exceeded, it's going to be a mess." We have to assume that the fairy godmother (henceforth abbreviated FGM) understood the nature of this ball. It wasn't simply a party where the prince was going to be in attendance. No, it was a party advertised as a one night, full season of "The Bachelor" where the winner potentially would marry the prince. That was the game and FGM was certainly aware of it.
Because of her past Cinderella had become conditioned to unquestioningly following orders; she had to or else she usually received more orders as punishment. So I don't think we can fairly blame her for not thinking through the possible contingencies, right? When the chimes started a'chime'n, Cindy's pre-programmed nature to obey kicked in and off she went. Most people will stop if a palace guard orders them to. She ignored a directive straight from royalty. This chick was a zombie.
Anyway, what FGM should have said was...
"If things aren't going so well, hit the trail before midnight because the spell will break, BUT if you're sure you're getting the final rose, just stay with the prince. When your dress reverts to rags and he asks, "What happened?!", simply say that the clerk must have forgotten to remove the ink tag. Then he'll take care of everything."
But since FGM didn't think this thing through, even if Cindy won the final rose, her frantic departure jeopardized everything. Toward the end of the film we see just how fragile these glass slippers are but you know what's even more fragile? - the FGM's witts! I mean come on! Look at all the possible points of failure here! What if she had smashed her remaining slipper on the cobblestones? What if the stepmother had successfully kept her in her room? What if another pretty girl had the same size feet?
Had it not been for several things coming together for her in the end, Cindy would have lived the rest of her life in servitude to some real jerks. It turns out that a higher power than a fairy godmother had a hand in this story.