Gamora always had good in her, it just took the "good Nebula" to get her to flip sides.
Captain America has been the only one ever able to even hazard picking up Moljinir other than Thor, and also wielded it in the comics in the past when necessary. The fact that he did was pretty much awesomesauce albeit expected by anyone who's ever read the comics.
Nebula was intertwined with her current time self due to her cyborg modifications/circuitry when she was in the same time/space, but it's not like dispersed computing where both of them were Unity together, they were just basically mesh networked... You shoot a PC on a network that's giving you problems, doesn't mean the whole network goes down, nor any data lost other than on the system you nuked.
Loki's "incident" was bypassed due to going even further back where they had a twofer of access, both to a means to return and sourcing the cube. That cube doesn't allow time travel, so while in that reality he got away with it, it may play in further at some point but I doubt it as it's a non-event.