Well, considering the Altmer are attempting to research and harness the power of the two moons, and then considering the Mane can only be born under a certain moon, it makes sense that killing the Mane might enable a certain acceleration of this understanding and eventual goal of Lunar manipulation. Mane-ly (hehe) because that would give them an undisputed control over the Khajiit, who are dependent on the moons of Nirn to survive.