Well its not just the zoners who need their cap ships removed. If they do retcon capships for zoners then they should do it for a couple of other factions too. (Which does look like a faction or two I am in will have them removed)
The other choice is that the zoners can keep their toys but with massively reduced weaponry and perhaps even some armor. These inRP changes can then be reflected back in the ships usage as a Colonization, exploration, transportation and mini biodome set ups. Sorta how (star trek example coming) Voyager, Enterprise (NX-1 and D/E) Had hydroponic bays in them.
They can set up these big ships to act as mobile freeports inRP which is largely what most Zoners say is their justification for holding one. Id advocate removing heavy and primary turrets but perhaps buffing the amount of secondary turrets so that it isnt overly susceptible to snubs.