Agreed with the OP. This mission left me feeling dirty. One of the overwhelming tenants of Star Trek in every incarnation is the idea that actions have consequence. Starfleet officers typically act in standing with their moral compass. This is just not the case here.
Ironically enough, one of the episodes shown during the SyFy Star Trek marathon celebrating the release of STO, was the TNG episode: The Pegasus...which deals with just such a moral quandry. Thankfully, Picard & Riker were able to finish the mission and get XP without going against their better judgment.