Although I'm not crazy about him as a character,I have to give it to him!
Danzou has been one of the real logical progression in interesting story left.
He values the village above everything else. He doesn't care about Sasuke, Doesn't care about Pain and his 'true' identity, Doesn't care about Madara's 'true' power. He's obviously thinks the best way to defeat Pain doesn't involve Naruto.
Most likely, he has some kind of strategy to use against Pain that involves some of the Root members. He was the man that competed with the third for the position of Hokage so he must have been pretty powerful and probebly was tactically sound. I knew that Danzou had something good up his sleeve especially since he tried to give Orochimaru all info on regular Anbu.
I think many of the readers would expect him to be evil or betray Konoha big time, but I strongly doubt it. He obviously didn't forget what happen 15-16 years ago when the Kyubi attacked Konoha and he isn't confident that Naruto will be able to keep the Kyubi quiet and calm.
Believe it or not, Danzou being sneaky bastard is needed, because of that joke of a Hokage.
Tsunade that have no reason been an hokage in the first place making a decision base on her emotion. She should know now is not the time to try to do 'the right thing'. How thoughtless she can be, to think Naruto can take on Pain right. Of all people, she should know that Pain is not a joke, he defeated Jiraiya, the second strongest of the Sannins and her former Teammate.
I also think it's hypocritical to say that what Itachi did (Killing off 100 to save 1000) is right and to say that what Danzou is doing is wrong.
Besides, that f*cking frog had it coming, with that ugly expression!
Danzou's final goal is currently unknown, we can't assume that he wants Konoha to fall, just because of his approach to treat the entire village like tools. IMO!
Also, Tsunade's disrespectful act towards the elders was so NOT wise!
Now they'll act on their own behind her back, and most likely be on Danzou's side. So it would only make easier for Danzou to go further with his ulterior motives as I would assume.
Why els would he prevent Naruto from coming back. Your village is getting destroyed and to dangle Akatsuki's "holy grail" right in front of them isn't very smart. If Naruto was captured then you would be at a severe disadvantage... your village just got annihilated, countless ninja's were killed, and now, you're hastily forced into an unknown conflict.
You have to take more things into account then personal ambitions/feelings which Tsunade clearly was unable to. People need to understand Danzou's position, Tsunade has little respect for him and she despises him, so do the rest of the village, while this man has been standing behind Konoha in so many years. He was in the shadow of people like Sarutobi and Minato. He deserves all the respect.