Deleting the user account from Active Directory or User Profile from the UPSA in SharePoint will have no adverse impact on metadata.
You could delete them from the User Information List which you can get to by navigating to https://siteUrl/_layouts/people.aspx?MembershipGroupId=0
, finding their username, and removing it from the site collection. This will have no impact on metadata for items in the site but will remove them from the User Information List.
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