I'm going to repeat a post, or at least some of the arguements and comments I used on the Sexism in the CS thread because they seem fairly relevant in this thread as well.
A lot of this leads into another major CS hang-up - human purity.
The CS has at disposal the capacity to create nearly limitless numbers of perfect cloned human embryoes, fast-grown, and gene modified for better combat survivability, enhanced strength and reflexes, yet they focus on external augmentation, artificial contructs, AI systems, powered armor and cybernetics. They even used to have taboos about juicers, and limit gene modification to non-humans (dogboys etc.).
Given the choice, based on their previous track record, the CS would very much prefer to increase their population the 'old-fashioned' way. For this reason, like any good socialist state on a war footing, they will discourage women from joining the military, but not forbid it. They will have lots of propaganda promoting 'traditional' gender roles, and the 'vital' contribution women are uniquely suited to facilitate in the great CS war machine - babies.
Put simply, the CS is extremely uncomfortable about anything 'non-human'. This discomfort extends to some degree to Psi-Stalkers, Juicers, and Crazies. Just the idea of Janissaries will seem abhorent to the majority of the CS populace.
Janissaries at a very basic level go completely against the few high ideals the CS has. Namely humanity and the survival of humanity. If things go so badly for the CS, that the CS has no choice but to resort to gene-modification of this nature, then they have already lost.
Then there is a control issue. A Skelebot can be de-activated or remote detonated. A SAMAS pilot can take of the suit. A Borg can retire with non-military grade cybernetics. What do you do with a Janissary when you don't need him anymore?
What happens if the Janissaries fighting in the name of normal humans come to the realization that they are a superior life-form than the weaklings they defend?