One cannot justify an omnipotent God in the Christian sense of the word to coexist with free will. So, in other words, no; under our knowledge of philosophy thus far, it is impossible to justify free will and divine foreknowledge existing together, but divine foreknowledge is not the same thing as fate. Perhaps this is one of the changes made to an ideal universe?
The choice offered by Christianity is essentially this: Believe this and you'll go to heaven. Don't believe it and you burn in hell, but it's still your choice. That's like putting someone at gunpoint and saying you can give me all your money or you can die, but it's still your choice. This is the viewpoint taken by the literalist faction of Christianity, anyway; I say it can't be justified because no solution offered has satisfied me, which renders it a matter of faith. I once thought about a framework similar to the Chrono series, in that God knows all possible timelines, but if he doesn't know what you will choose he isn't omniscient. The fact is the guy with the gun has the authority, and he's going to get your money one way or the other.
Using this train of logic, vehement atheists often portray God as a sadistic monster; a monster much like Lavos, actually. This is the primary line of thought used to refute Pascal's wager. Chrono on the other hand extoles the virtue of free will, and argues that victory against Lavos IS a human action, seeing as the Entity is made out to be hypocritical and selfish in Chrono Cross. Even though the Entity has a hand in Lavos' destruction, it didn't directly attack the beast. It took humans who were strong and courageous enough to decide to do something about it for Lavos to be destroyed; all Crono had to do to thwart the Entity's attempt at fate was to decide not to fight Lavos. If atheists are correct in their logic of an evil God, he will be a virtual Lavos clone.
All who've played Knights of the Old Republic II will remember Kreia's attempt to kill the Force. The Force is said to have a will, but if the Force has a will, then sentient beings aren't really acting freely. Of course, without the Force there can exist no life, and so the entire universe dies just because someone feels like being independent. That isn't really a logically sound course to take: if people don't know any different, then who's to say they don't have free will? If they can't quantify or observe the forces guiding them, their will remains. The attempt to touch the Force is the same as the attempt to get closer to God, to be part of something larger than oneself; so people can find purpose. It's hard to say that the Force is the same thing as Lavos; the Force desires life to grow and flourish, while Lavos desires life to bend to his will.