Currently, playing heimer is punished in this regard. If choosing a champion just in an of itself, regardless of role, gets "punished" as you call it, then I would argue that is an issue.
By the way, how do you think the community "punishes" a player? From my experiences, they have two avenues, Harrassment, and throwing that game. They usually go hand in hand. I've seen it happen myself, so telling me it doesn't is a flat out lie. Not even in isolated scenarios either. Didn't get their lane of choice? Time to Flame! someone chose a champ I don't like? Time to Flame! Someone took a different choice for support than the classically expected champions? Time to Flame! In this way, the community forces the meta down the throats of all, and It happens all too often to be the vocal minority.
Heck, I get heckled in BLIND PICK for going Heimerdinger. I am 100% fine with any role for him, and am willing to fill (I've even done adc Heimer. Not great, but there are worse choices). It doesn't matter, I still get heckled.
So yeah. there is a problem. Bending knee to the community because they will rage and throw super hard is a bad experience for all 10 players, yet the idea of blindly following the meta perpetuates it. It isn't about "being hipster", its about how 1 guy made a choice he should have the right to make, and gets flamed and loses all semblance of teamwork for it. That isn't fair to the others who have to listen to the rage, it isn't fair to the people who want a serious game, and it REALLY isn't fair to the people who want to play something they know they are good with, but that thing isn't meta.