Ultimately, does the presumption that the PCs must ally with evil creatures in Savage Tide screw over players with paladin characters?
That would demand entirely upon the assumptions.
Do they do it to aid evil rise, or to crush evil, and in the process screw other evil over.. ;)
Certainly you could make life difficult for the paladin, or overtly easy.. the best route would be to remind them they are very very close to damnation.. and as long as there are some sacrifices here and there it will all turn out just well.. more or less anyway.
No reason you couldn't turn saint, and with that preserve a good part of your powers should there be a slipup..