Can I submit a paper under an alias so as to avoid trouble in my country?
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.