So thinking about this and I know it's a retcon. According to the Ancient One the time stone created and protected what we know as the flow of time. It was taken during the battle of NY shortly after Coulson died. Obviously things also changed when Loki took the tesseract.
If the Loki show is going to be it's own time thing with it's own Loki, Could AoS now be a branch reality from that point as well?
The big change in their reality would be Thor 2. They did do cleanup at the convergence site I believe. That site doesn't change, what does is Loki's involvement, but that doesn't mean Thor couldn't prevail a different way. It also changes anything that would bleed from that into Ultron and the Helicarrier. However, Ultron really didn't have anything to do with Loki it was Tony's creation. Loki's disappearance wouldn't really impact Cap 2.