The bug was simply that whatever I did on the end of the second civil war, all my characters save two (the young Consul and a kid) just died, whatever I did. The moment the end of the civil war fired, everyone died. Every. One.
This should be fixed in 1.5.2, its the bug mentioned where if the revolt ruler is on a ship it results in some unfortunate things... If you still have the save it would be great to know if the issue persists for you now