Realistically, assuming you deliberately don't field weak teams on purpose to rest the players for the league, I would expect PAO doesn't lose every match. For each win it's 200K, each draw 100K. If you win the group, another 400K, runner up 200K. Adding all of the prize money up together with TV and stadium revenue for the matches, and you could be looking at 3M to 4M easy.
For a club that isn't flush with cash, that's a significant amount. I agree what you want is the CL money, but realistically, how on earth are PAOK, PAO or AEK going to win the title ? I just don't see it happening, although it would be nice to see a different team win the title for the first time in 187,000 years.
So, it's a case of, take the EL semi-seriously and get 3M or 4M, or take the gamble, and maybe if all the stars align (and there are lots of stars that need to align) you get the CL spot. It's a big gamble.
I get that if PAO were in serious title contention, might rest players vs the EL, but I don't buy not taking this qualification game seriously. It's as simple as "here is a team that is inferior to you, if you beat them, I'll give you 2.5M Euros". Who wouldn't take up that offer ?