Yes, it does need to be changed.
The poster above attempting to “defend” this degenerate/unintended gameplay is probably one of them 
800+ honorable kills in a completely one-sided 3-4 hour match doesn’t make sense, it’s a huge outlier compared to the other epic battleground maps. It’s not “normal” at all.
Again, we’re not talking about a true “epic” back-and-forth match that’s fair and balanced/fun for all the players… we’re talking about a premade group on voice comms “trapping” an entire team at a particular graveyard and just killing them over and over for 3-4 hours. Such gameplay doesn’t sound like “play nice, play fair”.
You can’t even pull off 800+ HKs in Alterac Valley with it’s 700 reinforcement count and reinforcement-generating nodes similar to Quarry/Oil Refinery.
Blizzard had the common sense to add some sort of hidden “reinforcements decay” to AV (the retail version anyways) to prevent excessively long games. But Isle of Conquest can literally drag on indefinitely due to the side-nodes, seems like a major oversight on the part of the devs.
But anyways, a simple “time limit” added to Isle of Conquest would solve the problem. 45 minutes sounds reasonable.
As for what happens if neither team is able to get a boss kill, the winner would just be the team that has more reinforcements when the timer expires.