Here's the problem with Endgame. In "Eye of the Needle", only 7 episodes into season 1, the Voyager crew refused an offer to have their expedition to the Bad Lands prevented because they had already made a significant impact on the lives of people in the Delta Quadrant.
So, the precedent had been set that you shouldn't undo "history". Yet in Endgame, there was suddenly no problem with undoing 20 years of unseen Voyager history. If the immorality of changing their own timelines was being ignored, then it would have made more sense to stop Voyager from being stranded in the Delta Quadrant in the first place.