Cleft lip is an unfortunate occurrence, however it is not ears that pop out too far, so please don't try to compare the two. I'm sure there are terms for the levels of cosmetic surgery, but clefts are probably at about a 10. The procedure is done to complete what nature missed. Its not elective to just do something purely cosmetic. As another poster said, its more like getting braces for teeth.
Man up? Hardly. Parents teaching their child confidence? Yes. Teaching their child that he is beautiful? Yes.
Dealing with bullying, and becoming more socially dynamic leads a person to be more secure. I dealt with bullying, more like this kid than you. You had something that I'm sure was far worse. I was a fat kid who was beatup & spit on around the clock. Had my pants ripped from underneath a bathroom stall while taking a #2. Good times. But over time, I learned to call out the elephant in the room, and be comfortable with myself. Which gave bullies no more fuel to feed their hateful ass fires. I love my parents for that. At no time did they make me feel like I was the one with the problem, but it was the bullies that had the problem. Got into sports, made friends, ended up slimming down due to activity.. and the rest is history.
And when I say pussification, again, its meant to say that we are dealing with normal-every-day problems in amazingly overprotective ways.