Nope. What he's preventing from happening doesn't happen. I see no problem with that, it just means it's very succesful in what it does. And besides, it's not true that nothing like that ever happens in the MEU, because it does. The Leviathan witness it numerous times, the Catalyst confirms it before coming up with it's solution
And that's exactly what happens in the ending of ME3.
Time to uninstall MEHEM.
The problem is that the ending is supplanting the original conflict of the entire series with something entirely different, one that the player has no attachment to and, even worse, undercut by the story itself (consider who the AIs in ME3 are: EDI, who loves a boy; and the Geth, which the game beats us over the head with how nice and sparing of organics they are). This leaves the new, more complicated conflict being explained in the last 15 minutes. This makes the ending feel disjointed and jarring. Just to give an example of how disconnected the ending is to the rest of the story, the Geth/Quarrian conflict -- which is our microcosm of the entire AI vs organic conflict in the Mass Effect universe -- has no impact on the ending sequence, nor is it even mentioned. The ending just feels isolated from the rest of the story, when an ending should be an accumulation and climax of what came before it.
As for the Catalyst, it does not stop the cycle, the Crucible does. Even though it acknowledges that its solution won't work any more it proceeds with that solution anyway in the Refuse ending. Even worse the Catalyst a minute earlier was so committed to this notion that it was willing to let Shepard destroy it and all the Reapers, although that would completely oppose it's original programming. Unfortunately, Shepard doesn't pick up on this and ask the Catalyst why it just can't leave or order the Reapers to self destruct. The only difference between this and the Destroy option is that the Crucible is used.
Synthesis, sums up the ending pretty well. The ideal solution (at least in terms of War Assets i.e. how well you played the game) is something that was never brought up in the entire series (in all of science fiction really, how often is there a fusing of organics and synthetic DNA). I mean it's nice sounding, but, boy, does it feel anti-climatic.