Yes. The change has been announced a couple months ago and is permanent (Well, for now..maybe next year things will be different). Don't expect the 20:30 flight to re-apear this summer.

Olympic has responded with extra flights. They announced the following for the summer:

AMS-ATH
OA150: 10:20AM
OA152: 20:30PM

ATH-AMS
OA149 06:30AM
OA151 16:00PM

So they introduced an extra flight, and, notice that the schedule is almost exactly the same as the 'old' KLM schedule. KLM changed their morning flight from 9:30AM to noon last year.

I have bugged KLM quite extensibly about codeshares for the new Olympic OA150/OA151 flights. These have (At least for me) excellent departure times. The answer so far has been: Most probably not, codeshares are generally published earlier. If by now they have not yet been loaded, chances of it happening are very very small. So don't count on it.

Together with the huge price hike of the KLM flights this summer I am now booked on AF and OA mostly. No status with OA but an early arrival into ATH (Before 15:45) is more important for me. Later arrival means a missed connection with hours of waiting, and since I fly up and down about twice a month that kinda kills the mood.

As for CSA: They used to have two daily flights. A redeye and a daily flight. The daily one used to be my favorite (and cost-effective) alternative to KLM. Last year CSA reduced their flights to one daily, the redeye. And now this one is/will be dropped as well.

OP: One alternative for you might be Alitalia. In the summer they have quite a few flights into Athens. You can also combine KLM and Alitalia flights, although that has to be booked through a 3rd party travel agency. I used to take the 7:20AM (KLM) out of AMS, change in Rome, with arrival around ~14:00 (On Alitalia) in Athens. And back with the direct KLM flight at ~17:00.