If taking Mjölnir from when they went into the past would of meant Thor wouldn't of been able to use in at all in "The Dark World" But since Captain America was able to bring it back and not disrupt the timeline, yet how did Thor know that Cap was worthy or even know they had to bring it back since it was only explained to Bruce/Hulk when he went back to retrieve the time stone?
I guess the simple answer to this is just... We're talking about Thor.
In the MCU he's a character that's always acting in a rather dynamic and direct way, just following his gut feelings. What's that? A bad guy!? Punch him in the face!
As such I can totally believe him just taking the opportunity without a second thought, following a typical "will figure out something later" kind of approach.
You missed the main point of the movie.
They took time to explain that this is not Back to the Future.
You can't change your own past.
By going back to the past, the team created 4 alternate timelines). Time is definitively changed in those timelines. (I hope the future "What if" show will explore some of those timelines).
You might be able to set the timeline on a very close track as before, by setting everything as it was before.
But it is impossible after the events of the movie. Everytime they went to the past, they broke something.
And you don't need to.
You don't need to undisrupt the timeline. All you need to do is to bring back the infinity stones at the same moment. You don't even need to bring them back in the same place and giving them to the same people.
So it does not matter if Thor saw Cap bringing back the hammer, or if Cap put it discretly in some empty room while no one was watching.
This is a new timeline that will never be the same.