Danzou was planning this stuff from the beginning. Remember how he killed that messenger frog?
"Now the Nine-tailed fox is out of the way" this is what he said as he killed the frog. He obviously didnt want Naruto to stop Pein from destroying the village. Which means he plans to blame the destruction of Konoha on Tsunades lack of competence.
If Danzo didn't kill the frog, Naruto would have been alerted much sooner. He would have then headed to Konoha in time to lead Pein away from the village. Damage to the village would have been prevented. Lives would have been saved. Tsunade would have been proven right. Naruto would have been made a hero. Peace would have come to Konoha and everyone would be happy. Everyone except Danzo.
Danzo wants to become Hokage and in order to create that chance he needed to make tsunade seem incompetent. What better time then when the village is under attack.
Now because Danzo killed the frog Naruto showed up too late. The village has been demolished and many Ninjas have lost their lives. Tsunade was also unable to stop pein. If Danzo were to jump in and kill pein he could steal the spot light and blame all of konoha's failings on tsunade. The only thing standing in his way right now is Naruto.
Personally Im really excited for the next chapter. I feel ive been waiting forever to see Danzo show his true colors and it looks like its about that time. *crosses fingers*