I don't own an SR9, but, the thing I haven't figured out is how bad a problem is the peening? I have not heard anything about the peening causing reliability problems etc. Granted, it is not supposed to be that way, but does it cause problems with the gun's functioning? I haven't heard of any.
I have a very early LCP, and they had a peening on the frame caused by the articulation between barrel and frame. Ruger recalled my gun for a safety issue, and at the same time ground off the frame section that was peened. All LCPs are now made with a cut out in the frame where the peening was common. The gun was fine after that, and I carry it in my pocket every day.
My point is, the fix on the SR9 may be a simple one. After the new barrel, the gun may be 100% and I don't think I would be quick to get rid of it.