There will be a slight difference, but if you want slow mo, that's a sacrifice you'll have to decide on. You'll have to do some post work to get them to match as closely as possible, but no more than any other shooting differences between shots.
Since you're using a camera that doesn't "actually" shoot ovvercranked footage, you'll have to do post trickery to get it in slow mo. That means you're specifically choosing to degrade the footage to get the temporal effect of slow mo. There is no way around that, it's a fact of physics.
If this is something that you're unwilling to sacrifice image quality for, either figure out how to go without the slow mo bits, or use a different camera.
If you're using final cut from the studio package, you should have Cinema Tools (or is it in Compressor?). You can do "Image Flow" slow motion with it by converting frame rates... not precisely how, but I have seen articles out there on it... Google is your friend. That will keep the resolution and do slow mo stuff by interpolating the frames between based on the existing frames and the motion from one to the next (like cel animation in cartoons - "tweening"). This can sometimes cause some funky artifacting around pieces in motion if the edges are indistinct (shoot with a higher shutter speed to avoid this - again, more light/wider aperture).
As far as frame rate, it'll end up the same frame rate, but the motion signature will be slightly different.