[quote=@Necroes]
Well, if it's going to be left up to me, I think I've got a [url=http://warhammer40k.wikia.com/wiki/Hemlock-class_Destroyer]plan[/url].

However, for it to work, I'll need some help. [@Klomster], my friend; how would you feel about performing a dark-mechanicum ritual on a couple hundred eldar? Of course, we'd need someone to perform some light surgery to get them ready. Someone versed in preparing mortal vessels for subjugation to the ruinous powers. 

Anyone here heard of death-masques?

[/quote]

While it is a fun concept, i cannot help but think that the Hemlock is so crap as a single ship in BFG and Rogue trader. It's not even fun :P
However, we're not playing one of those games here, and the skeleton crew might prove to be an advantage.

I wasn't planning on making such massive rituals as taking over the crew of an entire ship, not to mention eldar.
So for the moment i have no idea how i would write such an event to make it plausible.
I'd need help, in game.

A more pressing question is, how on earth would we catch an eldar boat? Not to mention board it?

As for taking over a ship with thousands of crew?
Most of those will be menials, whom have no interest in fighting. And how will we defeat the navy armsmen?
We'll just have to be crafty, since we can't take them in an open fight.
However, we have the warp on our side.