Can I submit a paper under an alias so as to avoid trouble in my country? I have done research on a topic that is very sensitive in my original country. I want to submit a paper to a (well-rated) Computer Science conferences, but I do not want to use my real name or university at all (neither for submitting nor publishing). Have you ever heard of such thing? How doable is it?
This is a highly sensitive topic, see Brian Borchers' comment:


  As a practical matter, even if the publishers of the conference proceeding were willing to keep your identity secret it would probably be relatively easy for officials from your country to determine your identity. It's likely that the publisher will want to avoid having any responsibility for keeping your identity private.


My advice: Talk to people from your university what to do. Ask trusted colleagues (which work on the same topic), university lawyers etc.

This question is too complicated to be handled by you on your own.