'My body, my choice' is an empty slogan, not a logic, and it can never be a sufficient criteria for judging or defending an action. It could be more completely and adequately expressed as 'My body, my choice, within the bounds of what the moral law permits', or perhaps 'My body, my choice, my personal accountability for my choices'.
In the case of breastfeeding, the overwhelming majority of cases would be ones where a decision to breastfeed or not is properly up to the individual mother. But even for something fairly uncontroversial like that, its possible to think of an extreme case where other moral factors would come into play. For instance, 'my body my choice' would not be a sufficient defence if a mother willfully starved her infant by refusing to breastfeed when it was viable to do so and no alternative means of feeding was available.