Saying "don't merge the servers" is not a solution to the question of what to do about plots with multiple owners if a merge happens anyway.
I'm not a big fan of the idea of merging the servers either, but I do understand that I don't own Istaria and a merge may happen with or without me. And if that merge does happen, I want to have input in the process so that it will possibly be less painful. A portion of a game's population being vehemently opposed to something does not mean that it won't still happen in the end.
These aren't separate businesses, though. They're two servers of the same game, and if Order loses players due to appearing to be a dead server, then that affects Istaria as a whole. If a merge does happen, then yes, it is important to do it right, but there is no way to merge servers in a game with plots like in Istaria that is painless for all parties. It just isn't possible.