Perhaps she realizes that Rand will surely call Perrin to account for his failure to bring Masema in. If Perrin can truthfully say that somebody killed Masema and he has no idea who did it then that puts him in a less dangerous situation than either trying to lie to the semi-crazy Dragon reborn (something I think Perrin would do quite poorly) or admitting that his wife murdered him.

Faile is smart in this matter. She put down a rabbid dog and shielded her husband from the responsibility.