Ordinarily, yes. An undead creature who is destroyed and then resurrected doesn't come back as an undead creature: it comes back as whatever it originally was, not as the undead creature. Nothing prevents it from becoming the same kind of undead again, of course, if the opportunity arises.
The Ghostwalk campaign setting (initially published for 3e, but an official 3.5e update exists) has a spell called raise ghost, specifically for bringing creatures back from the dead as ghosts. You don't even need to have been a ghost beforehand, as long as you're willing to come back as a ghost. Your soul knows that the spell will bring you back as a ghost, so you can refuse to return if you don't want that to happen.
This is not a general solution for undead beings, since it can only bring people back as ghosts, and not other types of creatures. In fact, it requires some reflavoring to work in other campaign settings anyway, because Ghostwalk's ghosts are not undead. But if it gets that reflavoring, it might be just the sort of thing you need for your particular situation.