I'd say use 2 different possible triggers to end the mission.
Event A - Hull Above XX Percent
when
-and
--(whatever your determination of the time to do the hull strength check is)
--(a check of if the hull strength is above the certain level)
-red-alert
Event B - Hull Below XX Percent
when
-and
--(whatever your determination of the time to do the hull strength check is)
--(a check of if the hull strength is below the certain level)
-do-nothing
<chained>
Event C - Player May Warp
when
-has-departed-delay
--Alpha 1
--0
-do-nothing
If the hull strength is low, then the player will have the option to warp out and back to base for repair/rearm. Then, the campaign file would branch to two different versions of the following mission, one which would be a Red Alert mission, with the branch tied to if Event A is true. The second branch may or may not use a briefing and be tied to Event B being true.