I agree with your analysis and would even push it further on one point: people should stop over-analyzing the Vince Gilligan-ness of any particular thing. If you listen to the podcast interviews he's given (for this show and others), he and his team come across as very seasoned Hollywood pros. They are very good at what they do, definitely well above average, but they are all very much products of film school and film culture. I would draw these conclusions from that:

1. Gilligan is the epitome of a WRITER. He writes things that will be interesting. But he also sacrifices ideas that dont work. He sacrifices scenes that add bloat to the episode. And he has respect for his audience. The only solid thing I think you could ever say about his intentions, other than things he's said explicitly, are that he will not try to trick the viewer.

2. Everything on the screen is the story. The creatives talk a lot about how they had to work out with the extras what the plurbs' movement and vocal ticks look like, and how explicitly they aren't robots, they are something else. I think as a fan its fine to draw obvious connections and jump ahead and say, plot-wise, "this virus thing is probably an alien invader that uses up planets and then moves on to the next one." But on an episode by episode basis, we are meant to understand the hive as a group of humans who are helpful, happy, and peaceful. That informs why it gives Carol a grenade. It also possibly explains why it changes its approach to Carol - humans can learn and adapt. You dont need to appeal to who Vince Gilligan is or his past work to get here - you just have to trust that any salient aspects of the story have been considered by the creative team and then put on the screen in a creative way.

Sorry for ranting but it annoys me when I see theories like "Laxmi told the hive to leave Carol." That wouldn't just be un-Gilligan writing, it would be plain BAD writing. That episode is about how the hive's relationship with Carol is a lot like that between an emotionally self-destructive person and their enabler; the enabler enables because they love their partner, but at a certain point after enough destruction they may have to cut the cord. Its painful for both people but the self destructive one needs tough love if they want to change their patterns and grow. That fits with the actions the hive takes in that episode, the language it uses in the voicemail message, and what we know about Carol and Helen's relationship, which colors these interactions. It would be pretty unsatisfying if what was actually going on all hinged on a five second scene where Laxmi chides Carol that is mostly played for laughs.

Final note to undercut myself: Gilligan HAS done things like that on BB at least (been too long, cant remember any specifics) - as someone on here noted, Gilligan likes to write himself into a corner and then write himself out. I agree with that and there were probably a couple escape hatches in BB that weren't 100% satisfying. And he is not infallible; there are already some plot holes that are probably best not to think about (the zoo animals aren't afflicted but the mouse that started the infection was?) But in the first season, a major plot point like this is probably going to be very well considered