Assuming nothing has changed since I last checked, during that 10 minute loading time the sub is still technically at the outpost and therefore would still participate in combat.
This makes sense for game balance. If this weren't the case, then I could dodge combat by "launching" my martyr 5 mins before combat, then cancelling the launch after combat.
So to answer your question: The martyr would still explode, yes.
"Can I make a suggestion that doesn't involve violence, or is this the wrong crowd for that?" -Hoban 'Wash' Washburn, Serenity