In New Vegas I was just able to take the conveinent "out" of the MQ by just going back to wandering after dealing with that Benny business. I don't think thats a good solution though, since it makes the whole central conflict of the game be put in stasis. Its 2282 in Alexander's game, and The Legion still hasnt even put more soldiers on the other side of the Colorado to replace the men they lost when I laid waste to all of their camps.
Im sure there'd be a RP-friendly way to ignore my dislike for the ending if it did turn out the NV way, but generally I would rather live with the consequences of my decisions instead of being told by a narrator about how everything happened years after I stopped doing things in the world for some reason. In New Vegas there were already plans to have post-ending content, you can find the remains of it in cut content with help from FNVEdit and the GECK, it just had to be cut for time. Obviously time is not a problem with Fallout 4, so hopefully we are shown, and not told.