She asked them to “leave me alone” so they left.
Ooh I see - not when she asked them to go away then said “Pirate lady can come back “but the whole period that covers Episode 5, 6, and 7, basically one third of the show - starting at the moment in Episode 5, after Carol injected truth serum into Zosia and the double bind of having to tell the truth but not being able to for internal reasons (probably vital imperative: speaking about reversing the joining when the joining is clearly everything they are) gave Zosia a heart attack. That’s when I realized the others may be smiling, but they are not nice.
(I’ve been thinking about this a lot after the remarks upthread 
)
We’re in the hospital after the truth serum experiment. As a time marker, we can see Carol’s arms are still covered in scars from the hand grenade but she no longer has the bandaids or the scabs on her hands from digging Helen’s grave. Carol is nervously squeezing a stress toy, clearly distressed about Zosia, and Others are milling about. They look at her and ignore her. When she gets into Zosia’s room they’re curt.At that point I’m thinking, they’re giving her the silent treatment, fair. Because Carol keeps hurting them, involuntarily at first then voluntarily!
But that’s not all: After eying a chair to stay in Zosia’s room, she decides to lay down in the corridor or hallway.There’s a long red hair bearded Hive guy observing her and as soon as she falls asleep they start moving everyone out (there’s that beautiful, haunting a cappella song and walking choreography). At any point during this, they could have said “Carol, we don’t feel safe around you, we need some distance for a few days/weeks/until we can be sure this won’t happen again.” They choose not to.
So they deliberately choose to let her wake up, go to Zosia’s room to find her gone (dead??), freak out (because we’re literally 8 days after her wife’s death and the end of the world), realize NO ONE is around and she has no idea why/when they vanished.
So she calls the landline and that’s #2 on my clues they are not nice: no one is responding. Not only are there no Hive puppets around but she doesn’t even have someone’s voice to talk to. They have a recording, always nice and pleasant, repeating the exact same thing (including “our feelings for you haven’t changed” which, you know, wouldn’t be recorded if they hadn’t, or ???) It’s genius from Vince Gilligan and his team actually, because that recording staying the same and being played in its entirety over and over and over drives a point too.
But anyway, Carol listens to the recording that states they’ll still respond to her needs but no contact. She takes that as a rebuke.
She has no answers so, clever and determined, she looks for one. She climbs to the roof of the Crowne Plaza Hotel. And from there she sees ALL the vehicles departing together, like a giant exodus. She’s aghast, stunned, furious.
Again, really, there was no need for them to leave the entire city (though from a viewer’s perspective the scene is incredible in its banality and oppressive impact, at least to me. Apparently it took them 2 months to plan the logistics of that scene??)