BTW, I voted for appointment over runner up. I lost an election back in DG1 (Civ III) and became Deputy Domestic Advisor as runner up. The Domestic Advisor and I held very different outlooks on what the Domestic Department should do and while Domestic Advisor was away I did things my way. When he returned he was not happy. Fortunately, since he was also VP he became President upon the latter's resignation and I got to run Domestic as I saw fit.

Anyway, the moral of the story is when there is a contested election due to ideological differences, do you really want the leader of the opposition as deputy?
There is a much simpler method that I've suggested from time to time in the Civ III demogames. If you're going to have deputies then elect them together with the leader, like we do when we vote for president/vice president in the US. Let the candidate for office pick his or her own running mate before the election and then we can vote for the ticket we like best. Then we have leaders and deputies in place when the election is over and we'll know the two are compatable.