You have to make a choice here because of SC profits, game economy, and to keep it from being exploitable. These are the two choices. There is no way to do this without picking one of the two...
- The timer runs out the full 48 hours before the clans can start another war
- The bonuses are reduced by an amount commensurate with how early the war is being ended. (I.E. End it in the first hour they are next to nothing)
You idea has been suggested many times, and if this is only about being hungry for more CW action then choice 2 would be acceptable. But so far all the guys wanting this are actually seeking to speed up their bonus payouts (I think half of them think they are clever and want the button for the exploit) so I have yet to see anyone willing to accept those terms.
So unless you can accept one of those choices its best the idea just die then. Ya know?