I have done a number of axles that had somewhat bad slots. I work the metal back down along the edges of the slots using a good heavy piece of steel as an anvil. You don't want the pound the crap out of it but massage it back into place. You want to pound some, fit the key and work as needed. Having GOOD keys is important as is making sure the axle nuts are tight. I start at 90FP's and tighten till the slots line up. Then check them a couple of more times after the car has been driven. Most wallowed out key ways are because the nuts have been allowed to get loose. Never back the nut off to line up the slot. To get the slot to line up if to far of, grind a little off the nut or swap them. T axles are strong but if you have to use a really long cheater bar..you can strip the threads. If the key way is bad in the hub, look for better hubs.
As Layden B said, it's having a good taper to the axle that's important, it's what really holds the hub in place.