As we all we know by now, before Eli dies, Eli tells you strictly to destroy the ship, while Kleiner thinks that it should be used against the Combine. This is quite a predicament and makes me wonder what Valve might do for Episode 3.
Should Episode 3 go interactive style and let you decide how to treat the Borealis? This would obviously determine the rest of the story because any choice would probably affect it greatly.
Also, sorry if this is old news. I just replayed Episode 2 for the gnome achievement, and this time I was actually listening to the dialogue and stuff because with all this Portal 2 stuff going around, I was more interested than usual.
I personally think they should use it, although I'm not sure what kind of power that boat may possess, Eli could be right about how there's no controlling it.