Why are you keepeng out AEK from the point deduction scenario? Did they not start the trouble?
No, there should not be point deductions for PAOK or AEK. The rules do not provide for point deductions for fan trouble that occur when the two teams are not even present at the stadium. Additionally, Olympiakos was going to get punished because officers of the game were attacked during or after the game. Fines clearly spelled out in the rule books, but not administered. Not only that they got reduced on appeal.
Now, the crowd trouble was disgusting, and the teams should be punished for giving out tickets to those fans. I think the fault is with EPO and the police that supposedly had everyone entering the stadium go through security checks. Also the police left the bridge connecting both fan bases without the police blocking it. Now how stupid can they be. Specially when exactly the same thing happened few years back in a game between Olympiakos Volos and PAOK. Believe me there were others that were very happy to see these incident take place, and they use to their benefit with media propaganda.
What should be investigated is how those hooligans managed to get those items into the stadium. But this has been happening in Greek stadiums for years and nothing has ever been done about it. Nobody apparently wants a solution to this problem.