Marks of Honor can be traded for purple gear at Deepspace K7 (check the consoles in the corridors). Marks of Valor cannot be used at the moment. We are supposed to get the NPCs for them with the 45-day-patch, and they should give us stuff which is especially useful against Borg.
Also, the weapons that are currently dropping from Rebecca, are supposed to be the new "vs Borg" weapons. Clearly they are not, and Gozer mentioned last week he would try to get the fix in before the next STF was released.
That will be a nice fix, because there was talk of the new weapons costing as high as 75 marks. That's alot, so it would be nice to get your weapons from Rebecca and use those marks for other things.