Yes, but Kefka was able to reach the Espers and kill them in Thamasa, and reach the Warring Triad in the Floating Continent to push them out of alignment, only because he was following Ghestal's plan. Not his own.
Ghestal basically lead him to the Espers and the Triad.
Jenova's 'agenda' was "DESTROY, KILL, DESTROY MORE, INFECT AND KILL EVEN MORE!"And the Ultimania may say Sephiroth controlled Jenova, but Sephiroth's actions wound up serving exactly the agenda Jenova wanted to push forward anyway so it doesn't really matter.
Sephiroth's agenda however, was "Merge with the Lifestream of the planet and become a god to rule over every soul."
Pretty different agendas if you ask me.