the star trek tecnology is more advanced. Better teleport system, desitegrator weapons. torpedos that can destroy a planet or a solar system... Ships that shoot with cloacking device on...
What torpedo's are they? Never heard that one. Anyway, they are nothing compared to Lances and of course, your Inquisitors all-time fave... Virus Bombs.... Exterminatus!
I'm afraid the USS Enterprise would not last long against the ships of the Imperium, they are God-damned tree-hugging hippies compared to drug-crazed Mongul Exterminators!.
Although it is sleak, fast and reasonably well-armed, Imperial ships are tougher and have far more firepower. Also, the crew of the Enterprise would not last 2 seconds when a boarding torpedo arrives, rapidly followed by dozens of heavily-armed genetically-enhanced killing machines. Anyone that resisted would be executed on the spot!
Kirk could probably be used, but he needs lots of augmentics, if he wants to stand on the bridge and give orders.... and he has to lose that spray-on uniform, its very gay.
Sulu would be slotted... he looks xenos, kill him. Scottie just ain't Mechanicus... slot him too. Czeckov(?).. xenos.... slot him. Spock, possible Eldar.... torture for a long time, then slot. Bones... useful, we'll keep him. Uhura (?) long-legged black lady... not sure of origins so torture for a little bit and then... slot.
Rest of the crew... penal colony.
Keep Pichard because he is just awesome... "Make it so". Troy... keep her cos she's fit. Worf... xenos, slot. Data, he's interesting. Hand over to Mech, disect, experiment... slot.
Ship... hand over to the Mech.
Use for scrap or target practice. Torture the shapeshifter before slotting. Slot the Ferengi.