If there is room, can you make a split ring that will crush the tube back to round? It would take quite a heavy ring to do so.
If you need a seal to work in the blend area of a welded build up, odds are that you would have some undercutting that would spoil the seal surface. Do you have metalizing capability? You could probably build it up that way and then bore & hone it back to spec. I don't suppose there is enough length to simply sacrifice a bit of stroke and just cut the bad end off? A new piston with the seals located back from the end enough to avoid the less than perfect area?
There are lots of places for this to go sour on you, so think carefully about how you proceed.