Stain tends to accentuate scratches, actually.
I would try steaming the scratches out before staining over them. This technique works pretty well on softer wood, but I don't see how it could hurt to try it on your oak.
Dampen a few paper towels and fold them so your moisture pad is a few layers thick. Place the pad over the scratched area and then place a hot iron onto the pad. (Make sure not to touch the wood directly with the iron or it'll scorch.) The iron will start to force steam into the wood and cause it to swell slightly. Hopefully this will bring up the lower regions of the scratch. Allow the wood to dry completely and then lightly sand the area again.
I learned this trick in shop class way back in 8th grade.
