All the Cobra senior membership pretty much loathe Serpentor at this point and want him gone. Cobra Commander may be a comical coward, but he was LESS a threat to their own forces when his temper flared.
Cobra Commander tries to create a splinter group from Cobra called The Coil. In the comics, The Coil are actually a group loyal to Serpentor, who revive after he is killed in a Cobra civil war