Agreed, use VPs if you run out of time (including a stalemate) unless your campaign states at the start that a stalemate is a tie regardless of VPs.
In future, it may be worth FAQing/errataing the Annihalation mission to state fighters don't count if that's all that's left (as an exception to the fighters counting for all other scenarios).
In future, it may be worth FAQing/errataing the Annihalation mission to state fighters don't count if that's all that's left (as an exception to the fighters counting for all other scenarios).