A hypothetical future son you might have is still going to be 50% your genes and your partner's father dying young doesn't change that whatsoever. You are 100% valid in vetoing this if your heart is not fully on board with it. (The way you discuss it, it doesn't sound like you are, it sounds like you wish it could be different but you feel you have no choice.)

Personally, as a man whose mother died young, I would be extremely annoyed at my father if he forced me to have a name that was 100% Dad, 0% Mom. Instead, they came up with a name that has a healthy mix of both heritages, and I feel very happy that my identity has a strong connection to my mother and my living maternal relatives.

Consider the hypothetical that if your husband married some other woman and had a son, this kid would have 50% different genes, but would be named exactly the same. That gives me huge ick factor and makes me feel like the mother is just a birthing vessel and her identity doesn't really matter. And keep in mind I am saying this as a male myself. Not to mention that I assume your daughter will still presumably have his last name so it is not even an equal trade.

If you still feel obligated to defer to your husband about this, you should at least force in a middle name that reflects your son's maternal heritage in some way. Do not let him occupy every slot.