I think there's a tendency to overrate Martins on here, but I agree that he should be in the team ahead of Owen at the moment (if Owen wasn't injured, that is), if just on his Goals Scored tally.
The fact is, the only argument for including Owen in the side is that he is "a better goalscorer." There's no other element of his game that is particularly superior to Martins. He is less pacey, is generally technically inferior, and he doesn't cover anywhere close to the same amount of ground. Therefore, if he is also falling behind as a "goalscorer" - his one and only real strength - it's pretty illogical to say that he should be in the team really.