Again, nothing in the movie ever actually says that traveling back in time creates an alternate universe. The movie says that removing an infinity stone from the timeline creates an alternate universe and that you can't change your past and therefore Back to the Future (and various other time travel movies) are wrong. That's it.
You may interpret events as implying that time travel creates alternate universes, but we really don't know if that's true based on what's written in the film itself and we really don't know exactly how Steve understood what was said to him (which we probably didn't even see in its entirety).
Also, for the record, the Ancient One never says a thing about a branch reality which is missing, say, the Aether or the Tesseract, being bad. The only justification she gives for not wanting to live in a reality without the time stone is that she would personally no longer have access to her great weapon if she needed it to defend Earth from boogedy boogedies. If that's the only reason the time stone needs to go back, then the other stones are debatable at best and the soul stone in particular would likely never even be missed.
And in regards to the shield: Cap getting a new shield from his past really isn't a problem. All you have to do is imagine a single adventure somewhere with the Black Panther (aka T'Chaka) where he proves himself trustworthy (as that's literally what cap does) and the door is open. Or you could just as easily imagine Howard Stark held some Vibranium back/melted down some other old prototype of his to make a new shield. Heck, for all we know Old Cap could've literally just been waiting at T'Challa's doorstep after the battle and asked him for a new shield and a ride to the time travel machine and also, I want this to be a surprise, so don't tell anyone I'm coming.