The seat rails seem okay on my car, they are not too rusty or falling apart... I suppose the best way to get the seat rail back in straight is to bolt it to the seats first and reinstall the seats then spot weld it and take the seats off...
This is partly why I'm putting in new ones. My stock ones aren't rusty, but the stock rails are quite weak and flimsy. They are also known to break the spot welds over time (and hard driving).
If they have to come out, there's no good reason to put them back in.
And since there's no way I'm putting stock seats in it, it only makes sense to install rails made for the new seats. The stock rails are just too close together, so too much of the seat hangs off the back end. This also might be why they break the spot welds.
Of course, this is for a 6'3" driver, so your mileage may vary.