Such a large power void will need to be quickly filled.

Think of all the countries that would immediately start wars if all nukes in the world disappeared (India vs Pakistan, arab countries ganging up on Israel, etc.).

Remaining wizards will look for security - either forming new covenants, or looking for protection of strong rulers (and what would a ruler do being handed one of the last few nukes in the world?).

The extermination of all the top-level mages is an extremely interesting campaign start, but it might be difficult to pull it off believably. If so many powerful men get together the security should be overkill.

My advice is to have the PCs be kept well away from the initial action, e.g. staying at a tavern at the foothill of the castle where only the mages enter. In the middle of the night they see the castle collapse or go up in flames. When they go to investigate they encounter their guild leader and focus on getting her to safety, only later will information surface on what went down in the castle.

As for motivation for the BBEG - I'd go for the Well-intentioned Extremist trope (http://tvtropes.org/pmwiki/pmwiki.ph...ionedExtremist). One (or more) of the top 100 mages (or someone from 101-200th place) want(s) to change the world for the better (get rid of wars, disease, feudalism, introduce a utopian society ruled by mages, etc.) and this can only be done if the conservative covenant is eliminated.