I don't think that it needs to be protected for you to use it as a HQ facility.
Instead, make sure it's powered, open to all and assigned to the faction.
When I was emptying the faction of protected assets I unprotected it with the other facilities and made it over to myself, it allowed me (the owner at the time) to remove it, I have since returned it to The Darklights.
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\"Rescue the president, Rescue the hostages, disarm the terrorists...\"
\"Rescue the president, Rescue the hostages, disarm the terrorists...\"
\"Rescue the terrorists, disarm the president, and kill the hostages...\"
\"Disarm the hostages