I'd suggest trying war/peace diplomacy system similar to the one used in EU3. The main features:

1. War alliance blocks with the principal war leader faction and minors.
2. Minors can sign peace agreements for themselves but not on behalf of the entire faction.
3. Majors can sign peace agreements on behalf of the whole alliance.
4. Occupied territory stays just that: occupied (cannot build, cannot train troops) until ownership transfer is confirmed (or not confirmed) in a peace agreement.
5. If a minor waits for the major to sign the peace agreement, minor's interests are most frequently ignored.

With this system: more game turns would probably be needed.