Just as the DM can stupidly choose to have the monsters ALWAYS fight to the death, the DM can choose to ALWAYS ignore morale rolls, or choose when to make them in the first place. It's not a rules problem - it's a DM problem.
Rules like morale simply cannot hope to handle all the subtleties and innumerable variables that determine who fights and for how long as readily and sensibly as a live DM. The DM controls ALL decisions for every NPC, every monster, just as the players control their characters. The DM should only relenquish that control when it is wrested away from him by in-game magical effects, just as any player only gets told by the DM what his character will do when HIS control is similarly affected. It makes no sense for the DM to turn over actual CONTROL of the game to such a weak, non-comprehensive mechanic. Just because a given DM can't/won't do properly what he is there to do in the first place isn't a good argument for general mechanics like morale rolls or aggro to try and force him to do it.