Given that erek went on a mission to help the Animorphs fight Howlers, I don't think their programming prevents them from doing that kind of thing. It just keeps them from doing it personally. the Chee, like other groups, were underused. it took about 25 books before the Chee even started posing as the Animorphs while they were on missions. They should have started doing at least that in book 11. Granted they did have lives of their own, and I'm not sure exactly how many Chee there were, but if they started doing it later they could have started doing it sooner.