What should happen is the team being punished should have their fans banned, but the opposing team should still be able to have their travelling fans attend. Why should the team who have done nothing wrong not be able to have their fans there!!!
Security advice suggests that the home fans with nothing to do would either
a) try and get in the away end or
b) wait at the entrance to the away end and pick off the away fans.
So banning away fans too is done in theory to protect us. I'd rather run the risk personally.
Stadium bans, fines etc are useless. A deterrent would be a points deduction or better than that, expulsion from the competition. But then they'll have issues fulfilling their TV commitments.
I was in Bratislava when they played Besiktas behind close doors in the first game so had been paying attention to it as I had wanted to go. For what it's worth, I think Slovan Bratislava were hard done to. This stadium ban was because they played a Kosovan side in the qualifiers and Slovan fans held up a banner effectively saying "Kosovo is Serbia". Controversial yes, but Slovakia is one of the countries that doesn't recognise Kosovo, so don't think they should have been penalised.
They are undoubtedly a bunch of wrong uns otherwise though, so they could have got themselves banned for something else if the ban wasn't in place.