Other methods were not available, the broader medical community did not seem to object, the medical standards were less developed, it was more acceptable for physicians to experiment and learn as they went, some good came out of it, and Freeman did seem to believe in the efficacy of the procedures.
Some of these arguments are stronger than others. Freeman's showmanship (including a death of a patient for a photo-op in the middle of a surgery), and refusal to wear sterile gloves were against medical standards at the time. The broader community was misinformed, as anecdotal evidence of successful procedures was spread by supporters of the procedure, while the atrocious consequences of it were under-reported. Freeman believing that the procedures were effective is difficult to disprove, but we know that such an assumption depends on veracity of a man who has shown to not be a trustworthy professional, and we do know that Freeman knew that the majority of his procedures had significant negative consequences. Some good came out of not only Freeman's work, but also work of the regime-aligned Nazi scientists, especially in the fields of birth control, medical imaging, and aerospace; and this very extreme case illuminates that invention doesn't always justify the means. The argument about the evolution of medicine in the US is more convincing - indeed, the current evidence-based medical approach evolved over time from a much more experimental one. This can be seen in the change of Hippocratic oaths medics would take throughout history. The argument for no better treatment being available is also a strong one - we have a framework around compassionate use or compassionate access to experimental treatments when nothing else is available today. But overall, the arguments, except for a few, are weak with hindsight.
It is important to acknowledge that Freeman faced no repercussions for his actions while he was alive - neither legal nor the widespread moral condemnation he is associated with today. People truly did not know what to make of it. But I ask - if a crime against humanity is committed but it takes humanity some time to recoil and it goes unpunished, is it not a crime?
It's definitely a very interesting topic. I personally don't believe that Freeman didn't know what he was doing, or that he had no reason to know his work was unethical. A man of his age and education shouldn't be as naive. It's more difficult to blame the families, though in this case, the memoir and other recollections do say that the stepmother was probably motivated by a hatred for her son.