Reposting this reply, somehow it disappeared…
Hello and thanks for your question.
From FAQs:
When using Multisite is a user deleted from the Network or only the Site deletion originated from?
If the user is registered to more than one Site on the Network they’re only deleted from the single Site, their user remains on the Network registered to any of their remaining Sites. However, if the option “Delete From Network” is checked and they belong to only one Site then their user will be deleted from the Network because they no longer belong to any Network Sites.
This is also mentioned in the ? tooltip of the “Delete From Network” option. The focus of the option is to prevent Multisite admins from being left with Users that do not belong to a Site, which can only happen with Multisite.
I understand how this can be confusing on Multisite to both user and Site owner in some situations. They might not always want deletion from all Sites on the Network at once and yet some people might be looking for just that.
I will consider adding this option to allow the behavior you’re expecting.