...and another apology. Once I reread NA 33, you were right. Killing a Molecule Man starts the death of your universe. It isn't instantaneous if they are killed early, but it does happen all the same.
Your post and the reread cleared up my last issues. So the timeline is that Doom and Owen kill the first alternate Molecule Man. His Universe starts to die but it lingers for a while during which time Doom kills more Owen's. About 7 years into the process the Incursions start, likely triggered by the early death of the universe housing the site of the original murder. By that point the Universes start to really die off, one after another as the delayed time reaction really kicks in. The Beyonders notice this and attempt to put the experiment back on track via the Map Makers. Most of the Avengers run happens at this point, but before the final show down between the Avengers, Illuminati, New and Mighty Avengers we have Thor's Multiversal Avengers assault on the Beyonders, followed almost immediately by Doom's assault on the Beyonders.
Whatever Doom does (It looks like he's attacking them with a weapon made of stacked Doom Time Machines, a particularly nasty weapon), Doom's assault triggers the massive collapse of the multiverse. It is possible Doom's assault doesn't trigger the collapse, merely that Doom's assault was ill timed and the Owen Reeses went off in each of their universes. Whatever did happen, that collapse triggers the end of our Avengers run and the final show downs.