How to find balance between overconfidence and lacking confidence?
1) How should I view the interaction? Should I assume I am probably wrong? Should I assume that he is wrong? Another option...?


Researchers should have differing opinions on topics such as whether non-explainable machine learning techniques should be used in healthcare. 


  2) In the future, should I press the debate more rather than only asking a few questions and thanking him for the info? Would this be impolite at a conference? Would it be an unwise career move?


Such opinions should be debated, that's how research advances, and such debate should be encouraged, at conferences and elsewhere. Some researchers will be less willing to accept your opinion than others, only you can decide whether you want to engage with such researchers.


  Should I raise my disagreement when this occurs? 


If you want to.


  How long should I debate the issue if we don't agree? 


As long as the conversation lasts.


  If we don't agree in the end should I assume I'm wrong?


No. There doesn't seem to be any right and wrong here, just opinions.