The staking of a carrier key is a controversial subject on many forums, which I find interesting because it really seems like there are better things to worry about. Not that it's okay to have the key come loose, but I have personally never seen one come lose that was properly tightened to start with, staked or not. I have read all the arguments for and against staking. I have had good luck with red Loc-Tite, but there are those that believe the carrier key and carrier get too hot for it to maintain effectiveness.
Been at this for 30 plus years and have run them staked, "Loc-Tited", and simply good old fashion "tightened screws".....have yet to witness a carrier key come loose. Maybe a better way of saying it is that I have never shot one of my AR's until they got that hot. You probably wont either.
My biggest thing about the "need to absolutely stake it" is that staked or not the screws can still move. I have had to disassemble a few that were "severely", very heavily staked {somebody had a phobia about the key falling out of their gun} and not too much more pressure on the Allen wrench spun them right out just the same as the ones I had to remove with "normal" looking stakes. Again, not much more pressure required than those not staked at all.
Bottom line, if it bothers you get a punch and hit them again...but I wouldn't worry about it too much. Given the choice, if I could only do one thing to them my one thing would be to get the correct Allen wrench and make sure they are good and tight.
I believe that staking the key was a mil-spec thing used from way back in the early days when the M-16 was shot a lot on full auto. Full auto gets then really hot, if the rifle doesn't get that severely overheated there is no need. On the other hand...if you feel like the carrier needs to go back to Ruger I suggest you find someone with a TIG welder because you are never going to be happy until it is welded.