The EU could have agreed to change its TLD ownershipo rules rules (which they actually have done recently, so the rules are not set in stone) to introduce a grandfathering-in provision if they had wanted to. Close it for new registrations but allow existing resistratnts to continue to renew.
But it seems they chose to be dicks about it, perhaps to spite the UK I guess. Maybe to send a warning to other truculent EU countries. I can't say I understand their reasoning. Perhaps just petty bureaucracy at work.
But now that the precedent is set, other EU citizens should be very wary of using .eu domains. There's no guarantee that your country will remain in the EU forever either.