Hioney

It's fair to think you need to disable the bosses or restart the server when issues arise. You could disable bosses proactively before any team engages them when server issues arise. If this is done just reset the spawn-cycle again to a shorter time or something. If you really want factions to fight for it/pvp, you will have to check for a consistent number or horde and alliance to be on place before you make it killable again. It's not fair to despawn a world boss when it's about to die because you think the other faction should have a "fair" go for it later. The boss kill would have ended up better killed WITH server issues than the later.