They are trying to keep her from becoming whole with Namine. And while they became whole, Namine would probably tell her to try to get Sora to become whole with Roxas.
Where the hell did you pull that one out of? Namine and Kairi fusing would actually be in the Organization's best interest since it would get Namine to stop meddling with them. Kairi has no powers over Sora's Memories; Kairi can't open Corridors of Darkness; Kairi couldn't affect Roxas if ever they finally get him back. Namine's a threat, and her fusing with Kairi would give the Organization one less thing for them to worry about.
Also, you're forgetting that Sora and Roxas already became whole
They fused initially as early on as the end of the Prologue, when Namine and Kairi were as far as possible from meeting let alone fusing, and then re-fused, but that was before they even reached the Castle that Never Was!
tl;dr the Org'd want Namine and Kairi to fuse. It's already "too late" about SoRo.