Ninja Assassin/WMG

Keiko was the mastermind behind it all...
Think about it. Why was she the only girl being trained? It's because she wasn't really the trainee, she was the founder of the clan, and Ozunu was a puppet. If their techniques can heal injuries, why not reverse aging (maybe even swap genders to make him/her more sympathetic), and (if Raizu had gone through with it) regrow a heart. The whole thing was her way of testing Raizo before making him the next Lord Ozunu...only, she didn't expect him to rebel and succeed.
 * She wasn't the only one, When Raizu was going to be initiated fully they gave him another trainee who tried to leave to kill. He also once said they must kill Raizu to "Avenge your brothers and sisters."
 * It does bring up an interesting point though in how the only two female ninja we see from the Ozunu have tried to escape (since we don't know where the one who tried to kill Rain in the beginning was I won't count her). Why do they keep getting girls if they keep trying to escape?
 * Because female ninja are useful, mostly because people don't expect to be murdered by an (often petite, in this case Asian) woman. Example: The female ninja in the laundromat, who would probably have succeeded in her mission if she hadn't been up against the star. Besides which, we don't know that all the female ninja try to escape, just that we saw two who did; which, for plot-related reasons, were Kiriko as Raizo's motivation and Nameless Female Ninja to remind him of Kiriko and kickstart his defection.

The People Who Were Trained by Ninjas List

 * Soap, Price, Jackson, Shepherd, and Ramirez from Modern Warfare (Price at least demonstrates the inexplicable ability to appear whereever he likes, and is no slouch in punching people. He, as well as the others, also has the ability to will his wounds closed and kill entire legions of commandos with just his fists and a knife.