"Code-cowboying" is just fine if you do it on your own time. If you were doing it on your own time and they had a problem with it, then they clearly have a problem. Otherwise, it's not as clear. Politics are a real part of life, and that's why many people flock to startups (in addition to hoping for a payday) and to doing their own thing. If they aren't actively doing it, then they are dreaming of it. While I don't side with those that say that you should become political, I think it's worthing knowing how to do so just to buffer yourself against those situations where you must.
The responses to this question were strange. Everything about them is promoting conformity to the very thing that puts out the fire in most young engineers in favor of conformity to "The man." I can't agree with that. There has to be another way.