No, Freedom of Movement only ignores circumstance penalties to speed and Repulsion is difficult terrain or just outright don't let you come closer.
I agree with Kyrone that Freedom of Movement doesn't automatically ignore anything that Repulsion creates, but the theme and intent of the two spells are in enough direct opposition to each other that they could justify a counteract check to see which effect takes priority.
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While under this spell's effect, the target ignores effects that would give them a circumstance penalty to Speed. When they attempt to Escape an effect that has them immobilized, grabbed, or restrained, they automatically succeed unless the effect is magical and of a higher level than the freedom of movement spell.
Success The creature treats each square in the area as difficult terrain when moving closer to you.
Failure The creature can't move closer to you within the area.
The things Repulsion does don't match the things Freedom of Movement is looking for. Difficult Terrain isn't a circumstance penalty to Speed, and not being allowed to move in a particular direction isn't immobilized/grabbed/restrained, since you can still move in other directions.
Repulsion is a higher level spell than Freedom of Movement, so I think it's a moot point. The fluff in FoM is clearly in opposition to the effects of Repulsion. I accept that in P2 that's meaningless, but in this case, the name of the spell overrides that for me. It's called "Freedom of Movement." Repulsion uses "move" words six times in its description. I could see a ruling in either direction and would rule in favor of fun or in favor of the players' will here and "move on." ;)