How did the Infinity Stones bring everyone back if the people aren’t dead in the stones original timeline?

The stones brought back everyone who died due to Thanos’ snap. This doesn’t include characters that died getting the infinity stones such as Vision, Black Widow, etc.

Basically Tony just undid Thanos snap when he whipped out half of the universe.

I think the simplest answer is that the Stones don't care; they are working on the wish of the person in that moment, and can probably see across time to know who to bring back.

Here's a bit more in-depth answer based on what the writers and directors have said (which I don't think makes much sense):

Normally, time travel doesn't cause branching timelines. Barton taking the ballglove didn't do anything like that (though it did duplicate the ballglove, leaving one in the past and taking one with him into the future). Thinks like Professor Hulk rampaging in the Battle of New York isn't actually a change for the original timeline, because it already happened the first time around, just no one knew it wasn't the Hulk of that timeline. However, taking a Stone out of it's time does create a branch, just like the Ancient One describes. But returning the Stone also eliminates that branch, just like she describes.

With that background, we can loop back to directly address your question, and come up with three possibilities:

1) The creators are trying to split hairs and argue that alternate timelines are different than alternate universes.

2) The MCU version of the Stones, while seemingly more limited in the scale of their power, might be able to work across multiple universes of the MCU.

3) Everything we've seen thus far is a single timeline, because they took the Stones back. Even though they hadn't yet as we watch, because of the joys of paradoxes related to time travel, they already had returned them as well, and therefore there wasn't a branch (except the one Loki created).