Naomi gave Tobias her permission to take the urn (I'll never understand that. What kind of mother would someone let take the urn of her daughter?), so she I'm sure she knew.
I actually thought it redeemed her, considering how irritating she was during the final arc. She loved Rachel, but she didn't understand what she had become. By the end Naomi saw her as most of the other Animorphs saw her. She loved her, but she was a stranger to her at that point; she missed out on her daughter's steady growth of her eagerness for brutality. I think her allowance of Tobias carrying away her remains was a silent acknowledgement of the fact that Tobias knew Rachel much better and, not to reduce or compare a mother's grief for the passing of her eldest daughter, that he was more affected by her death. She was his only solid tie to humanity and the only consistent human relationship he ever had.
So, kudos to Naomi for not being irrationally possessive like most other mothers would have been. I'm impressed.
