Assuming your script results yield one event per excluded user with a user field set to its login, you can do this:
sourcetype=something NOT [HRUserException]
That will take the results of the subsearch, for example these events:
1: user=foo
2: user=bar
3: user=baz
and turn that into this search string:
( ( user="foo" ) OR ( user="bar" ) OR ( user="baz" ) )
The NOT in front of the subsearch will exclude those three users from the search, giving you this main search:
sourcetype=something NOT ( ( user="foo" ) OR ( user="bar" ) OR ( user="baz" ) )
If your external command results don't have a user field yet you may need to rex it out of the results first.
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