Okay, let me break this down as best I can.
She assumed that Prince Charming would be the one to rescue Fiona, which we know didn't happen, considering the first film.
Correct. Harold even calls her out on it:
HAROLD: It's not my fault; he didn't get there in time!
If Shrek hadn't come along, some other knight could've eventually rescued her.
I'm less convinced about this one. I'd argue that it was reasonable for her to assume that nobody else would be capable of rescuing Fiona. We see that plenty of people had already tried to rescue Fiona prior to Shrek coming along, and all of them had failed, quite painfully.
She also assumed that Charming would be Fiona's one true love if he was the one to rescue her. There would be no guarantee of that either.
Correct again. But I don't think she assumed that at all. I don't think she even cared how Fiona felt. If it turned out Fiona didn't love Charming - which she didn't - she was prepared to drug Fiona with a potion that would force her to love him:
FAIRY GODMOTHER: Have her drink this [potion] and she will fall in love with the first person she kisses, which will be Charming.
Godmother put the spell on Fiona to keep her changing into an ogre every night as a secondary precaution to keep her in the tower
Wrong. The ogre-transformation spell was cast on Fiona by a witch, and was the reason she was put in the tower in the first place. There is no canon evidence that the Fairy Godmother had any involvement in that.
Since he's not her true love, he'd have rescued her and she'd still turn into an ogre every night.
Correct, but it's likely in that scenario that the Fairy Godmother would have used a spell or potion or something to reverse the spell. After all, she quite fervently believes that:
FAIRY GODMOTHER: Ogres don't live happily-ever-after!
...which, by the way, is another incorrect assumption of hers. They can, and do.