Winning via super weapon is irrelevant. That's not the problem. The problem is that it's a super weapon that the enemy knows all about, but for no fathomable reason does anything to neutralise.
You can ONLY win on the Catalyst's terms. It lets you win. Refuse eventually yields a win, but it's technical. The next cycle wins, you lose.
To labour the point, it's BS that Shepard simply buys into everything that Starjar tells her/him. Starjar couldn't possibly be telling porkies, it's not like you've got it by the balls or anything. Not like you've just parked a Galactic Reaper-killer on its doorstep. Why would it possibly lie to you......
Like I said, I can live with high EMS Destroy, just. It just grates that you go there knowing that it's based on the Bratalyst being incredibly stupid in even telling you about that option. A contrived technical win, handed to you via timely logic-fail on Space Casper's part. An intelligence that's smart enough to take down the Leviathans and every sentient race since, just happens to brain-fart at the pivotal moment in the game. Yeah.....right.