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.
They did do something about when they keeping sitting on the final component needed to make it work for centuries every time they invade the galaxy.
Remember with out the Catalyst aka the Citadel the Crucible is useless, and the standard Reaper invasion starts by taking the Citadel in a massive surprise attack while also destroying the galactic government followed by hunting down and exterminating whats left of the galaxy's civilization.
The only reason they didn't do that until later in Mass Effect 3 was that the Citadel relay was taken out of play by the Protheans, and then later Shepard killing Sovereign.
So they really don't have to sabotage the plans since their usual invasion plan makes finishing the device impossible.
And its not like they wouldn't notice that the plans call of the use of something that has the same name as the AI controlling them.
Besides an "unconventional refuse option" sounds like wishful thinking about a magical deus ex machina that can be pulled out at the 11th hour so as to get by fact the the Reapers can't be beaten without some ultimate weapon one of the previous cycles may have come up with that the games previously hinted at.