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With reference to this question the most upvoted answer says that in Avengers: Endgame the plan was to return the
Stones back to their timelines and not snap Thanos out of existence.
But how does this solve the problem when Thanos will continue to exist and still cause harm as he has access to the
Pym particles and can potentially travel back to retrieve the returned Stones. Isn't the only way to end this would be Iron Man making the sacrifice?
Because when the Infinity Stones are returned to their time lines the alternate reality where that Thanos and his army are from will cease to exist.
The Ancient One: The Infinity Stones create what you experience as the flow of time. Remove one of the stones, and that flow splits. Now this may benefit your reality. But my new one, not so much. In this new branched reality, without our chief weapon against the forces of darkness, our world will be overrun. Millions will suffer. So, tell me, doctor, can your science prevent all that?
Banner: No. But we can erase it. Because once we're done with the stones, we can return each one into its own timeline at the moment it was taken. So, chronologically... In that reality.... it never left.
Avengers: Endgame
Remember the scene where they have this conversation there is a diagram in the air, when the Ancient One removes one of the Infinity Stones a new time line shows up on said diagram but when Banner puts it back again the time line is erased.
This Thanos, his Children and the armies are from an alternate reality where the Power and Soul Stones were taken from. So when they put the Stones back into 2014 the Thanos and his forces would have been erased.
It's also worth noting, as Nathan K says in a comment, that the plan also stops the immediate problem of Thanos being able to get his hands on the Infinity Stones and snapping. They are removing them from harm's way.
The question asks about the original plan, so...
According to the original plan, there would be one and only one timeline. In this timeline, the sequence of events would have been:
Past-Thanos following the Avengers back to their present was not part of the plan. If that hadn't happened, then — from the perspective of "the past" from which the stones were borrowed — nothing would have changed. Thanos would have eventually gotten the stones as he did "before", "The Snap" would have happened, and it would have been undone as in Endgame, because it would have all been one timeline.
Presumably, Thanos finding future-Nebula created a second timeline. When he subsequently invaded the Endgame timeline and was dusted, he would have ceased to exist in his own timeline¹, which presumably means that timeline still has infinity stones, while the Endgame timeline does not (unless someone created a second set off-screen before returning the "past" infinity stones).
(¹ ...or if he'd won and just not returned to his own timeline. Being dusted ensured that he couldn't return.)
tl;dr - There was no way (a debatable point) to undo the events of the timeline as we saw it, but they could sneak over to other timelines and fix the majority of the effects of The Snap.
The main problem is the somewhat confusing theory of time travel that the movies used, which is based on at least A version of time travel the comics have used.
According to the explanation, when you travel in time, you do not travel into your own past, but into an alternate timeline in which your appearance took place. So taking the stones out of the timeline does not erase their existence in "our present", and does not negate Thanos being able to retrieve them.
So the recovery missions generate several new timelines where each of the stones no longer exist where they did in the main timeline.
But by returning the stones almost immediately after they were removed, the effect on said timelines is virtually nil. So for example, the Ancient One only loses the use of the Time Stone for a brief period, not long enough to fail to defend the Sanctum.
Thanos' time trip generates another timeline, one where he simply and mysteriously blinked out of existence. That timeline never saw him collect the stones, and never suffered through The Snappening. The Thanos we saw at the end of the film was not the same Thanos we saw at the beginning, but one from a divergent timeline.
