Nikolas K. Gvosdev of the National Interest tells me:

The basic comparison I can come up with is what would have happened in
2000-2001 if Israel had assassinated Arafat. Basically you’ve eliminated the
titular head of the separatist/terrorist movement, but since he really
didn’t control his ostensible subordinates, you haven’t dealt a “death blow”
to the movement.
Basically both separatist presidents of Chechnya and the one pro-Moscow
president of Chechnya have all died by being killed in combat or
assassinated. Not a great track record.
In death, of course, Maskhadov does become a martyr and I assume there’ll be
revenge attacks in Russia proper.