This actually makes a sort of sense out of why Gwen wound up leading Torchwood while Jack was gone, although I still believe she was largely the leader in name only - after all, in season 2 she still didn't know about UNIT!

I love the thought of Tosh and Ianto both knowing Jack had gone with the Doctor and working together to keep confidential things from the others while he's gone. Bet they don't even let on to each other exactly what they know, neither would break a confidence. They just carry on and run things from behind the scenes. =)