Drop it with him for now; he is so young he might not even remember what she said, and if you reintroduce the subject it will only make it loom larger and seem more important to him right now, when you aren't really ready to go into it yet.
One positive: Your husband said he would talk to his M. about it. Too often here, the daughter-in-law posts that the husband won't deal with his own M. on sensitive subjects. You're fortunate your husband will do so and takes the responsibility for talking to her.
Please cut her some slack on this. Bear in mind: She heard her grandson, iin her mind, reject her; she may have life experiences in which she previously felt rejected because of her race, and she may immediately have transferred that experience to what she felt was happening with your son's innocent statement. She, like all of us, is the product of her experiences, and if she has had painful issues in the past with being rejected because of her race, her gut reaction likely would be to assume that race is the basis of this rejection too - yes, even from a young child. She did not mean to bring up a topic that you're not ready for yet. And instead of getting angry with your son for what he said, she spoke to him in terms of love -- even if she was wrong about what motivated his comment. If you otherwise have a fine relationship with her, please try to put aside your own anger and sensitivity about her "making distinctions" and let it go. And bear her own past and experiences in mind when giving her some slack.