The Bene Gesserit are accomplished and masterful manipulators. They also have generations of experience in developing training programs that specialize in instilling discipline and loyalty.
Jessica's "betrayal" by disobeying her orders and having a male child instead of a female are intended to indicate both her strength of personality, and the power of her love for Leto Atreides, and is an exceptional, rare instance of disobedience.
However, for the Kwisatz Haderach, discipline and control would have been much stricter than a rank-and-file Bene Gesserit, even one who plays a key part in their breeding program.
The Kwisatz Haderach would have been carefully shaped and trained from early childhood, and likely would have been taken from his family through Bene Gesserit manipulation while still a child (the Bene Gesserit have already demonstrated that they can find ways to manipulate even the most powerful families, including the Harkonnens, in service to their breeding plan).
On top of that, it is almost certain that an Imprinter would have been assigned to control the Kwisatz Haderach, much like they eventually planned to do to the Duncan Idaho Ghola in Heretics of Dune. The Imprinters are specialized, trained sexual manipulators, using much the same techniques as the Honored Matres (although less refined) to sexually influence men and ensure their loyalty and cooperation.
Between the combination of upbringing, conditioning, and sexual imprinting, the Bene Gesserit would have had a Kwisatz Haderach who was at least mostly sympathetic to Bene Gesserit goals, and who would have been possible to influence in most important matters.