That was more of an inside joke poking fun at one of main reasons people didn't like Brand New Day then a commentary on your peace. It basically boils down to the fact that some people where upset because Marvel was officially ignoring Spider-Man canon instead of unofficially like that it has been.
[THE FOLLOWING IS SIMPLY A KNEE-JERK GEEK REACTION AND SHOULD NOT DETRACT FROM THE AWESOME REGARD I HOLD THIS IN]
You know, really Bruce should be the one to shut up here. Peter's parents are dead too (or clones or robots or something) and his Uncle got killed and it's (indirectly) his fault! So yeah, I think he's allowed to have a few regrets about it.