robbert, sorry for the headache you had.
Unlike many international or US airports, I don't believe you can get boarding passes issued within the secure area at MAN, at least, not on KL or CO. Perhaps AF can since they operate the lounge?
Did you ask at AMS about getting the return boarding pass? I'm sure they'd say "schnot possible" as a starting point, but I imagine this should have been doable?
I'm really shocked you had so much trouble; if you check out the Trip Reports forum, I just did a trip report about starting a journey from MAN and I had no issues. But this was Sunday morning travel, so that might skew things a bit.
Congrats on the op-up. AFAIK they are not policy, but I do get op-upped on MAN-AMS flights maybe 25-30% of the time. They are frequently overbooked both ways, so they compensate by either moving the business class curtain or simply op-upping.