I've used my real name from the start as a free software developer, Debian developer, and professional scientist and professional software developer; I've also been involved in some heated discussions in my more youthful days, but that's never been escalated into anything outside being flamed by someone. There's a tradeoff here, and I don't think being anonymous/pseudoanonymous is sufficiently beneficial to warrant it; there's a certain loss of trust in doing so, and it hasn't been a problem for me in the last 18 years of free software- and software development-related activity.
I know what you mean, I'm on the internet since '89 and used my real name on e.g. usenet too but you have to realize that today is different than back in the days on usenet and forums and IRC channels where flamewars were kept inside and seldom bled out to other areas, left alone real-life. There are certain areas where I don't use my real name (e.g. in areas that are gaming related) and that's simply because they can be hostile like we know from usenet, but at the same time they DO bleed to outside areas and can affect other aspects of your life, i.e. bleed into your professional life. Back in the days that was uncommon (if you were in a flame war with some people on some IRC channel, chances are if they contacted your work your boss would likely answer "IR what?"), but today it's not. The tools are there, and more than before the concept of 'identity' is different: it's no longer only your passport and the information in it, it's also your combined profile online of all the sites you frequently visit and leave your opinion. So it's best to be careful, e.g. not to use a real name in places which have nothing to do with where you're using your real name.