Ah, but would a dragon even be hostile to Martin of-the-blood?
Likely not, actually. Tiber Septim gave safe harbor to the remaining dragons near the beginning of the 3rd Era, and Battlespire suggests there was still at least one in service to the Empire under Uriel VII a few decades before he died. Given that Martin was dragonborn, I don't see why dragons would suddenly want to assert dominance over him and none of his predecessors since Tiber.
Unless part of the dragonfires ceremony involved the Emperor asserting the Empire's continued dominance over the dragons... but if the dragons' numbers were
that low, I don't see the dragons as wanting to pick a fight with a dragonborn. They may want to dominate, but they're not stupid.
Of course, none of that means Martin couldn't kill a dragon and take its soul if he wanted, but he doesn't seem to be the type of guy to do that.