I know.The Akatsuki and Nagato was because of Danzo and Hanzo's alliance. Hanzo asked Danzo for help in stamping out this new group.
But, didn't Danzo go behind Hiruzen's back to do that...what's worse is that he escaped without finishing the Job leaving a vengeful Nagato and potential threat. Didn't Danzo want to use that alliance to overthrow Hiruzen?
Letting your Village be destroyed on purpose so you can rebuild is dumb...what if the enemy has spies and decides to use that opening to finish your people off.
As for Shisui...wasn't Fugaku the man instigator egging his clan on...It might've been effective to turn him and use him to convince his clansmen.