Torah and moral issues

  I just received the following email and thought it worth sharing and hope to get some helpful responses

Dear Rav Eidensohn

I hope this email finds you well. 

I wanted to ask you whether you have ever written about an approach to reading the Torah when it conflicts with our modern sensibilities and moral compass. I am trying to come to some kind of resolution of some questions that my kids ask me. In particular, my son is learning the second perek of Kiddushin now and finds it very difficult to understand how the Torah could allow a father to marry off his minor daughter and even allow a person to be boel a ketana (my son told me that it works for a 3 year old) for the purpose of kiddushin (which I assume is permitted midin Torah but I am not sure). How do you understand that halacha from the Torah? Do we limit it to some time in the past and say that at the time the Torah was given, that was acceptable in terms of the morality of the day but that the Torah does require us to progress morally as well and that today - given the development of society in terms of individual rights and freedoms -  the Torah would not condone those types of actions either? And maybe that is why the Gemara that says that it is assur.  If so, are we limiting the Torah by saying this and saying that some of it might not be relevant today (maybe something like korbanos without a Beis Hamikdash)? Or maybe we say the underlying principles are still relevant but the details may play out slightly different in real life? Or do we say that the modern push to individual freedoms and equality are inconsistent with the Torah and that those issues, even if they sit uncomfortably with us today, are "moral" or "Hashem's will" and marrying a 3 year old girl is "moral" or a reflection of Hashem's will somehow and that we need to try to align our thoughts with the assumptions that the Torah appears to be making about these issues?

If you are able to share with me your approach to these issues (including any psychological insights you might have), or point me to some mekoros that might be useful, I would be very grateful.

Thank you so much