[Show spoiler]
The way I see it is that they prune variants when their existence might cause a nexus event that would alter time/dimension itself. For example, Sylvie was pruned because her future might have impacted not just her universe but also the universe HWR has made. That is also why Loki's time after he acquired the cube was erased. If he was left alone with the cube, it might have caused a massive nexus event.
That is why Kid Loki was pruned. If his story is to be believed, he killed Thor. That would have set off a massive nexus event where the current MCU would not exist.
Classic Loki managed to trick Thanos and went into hiding. Since he no longer was doing anything to the current timeline in hiding, he was left alone. Only when he stepped off planet, that trigged the TVA of his existence and what he could do to the timeline.
Think of it like a domino set up. One domino (variant) can set off a chain of events that deviates from a set path. Once you remove the domino, the rest of the dominos do not fall.
You could argue that HWR might have chosen Sylvie because of all the scenarios he has seen, she would have been the only variant who could take his place or kill him. So he pruned her out of necessity to start the domino effect leading to their meeting. Since she was a variant already, wiping her out wouldn't impact the sacred timeline.