With regards to Torchwood, I really think he doesn't know how much of a threat they might be to him yet. The only times they've been mentioned in his presence came in an off-hand reference at the party in 'Rise of the Cybermen', and at the end of 'The Christmas Invasion'. Where, admittedly, they were pretty nasty, but the Doctor had no reason to suspect he might be a target, or that Torchwood was anything other than a particularly high-tech missile defence system.

(This is what you get for voting Gordon Brown in, people of Future Earth!)