While I do agree to the general sentiment that jewish law need not fit in with "modern" ethics, I disagree with some of your points made in this post. All mitzvos are meant to refine our charachter and make us more like god. Yes, there are some that we may not understand at all or fully how they do make us better people. However, there are many that are intuitive in how they improve us, to the extent that if there was no torah we would still practice then. I believe that if we approach these mitzvos from the perspective that we only practice them becuase god say so and they dont have any reasoning behind them they will have minimul affect on improving us. Yes we would give charity even if it had nothinf to do with being compassionate and we didn't understand the benifit but luckily charity is an act of compassion and we are required to feel that compassion.
The problem with only doing Mitzvos because they make sense, feel right or are 'intuitive' is that you run into roadblocks when society's view shifts as it has over the millenia and you find that current scientific theory, or pop culture is at odds with your beliefs (ex. creation ex nihilo, prohibition against homosexual relationships, or abortions)
As to your point regarding Mizvos making us more like G-d, things get more complicated.
I was taught that you lead with your mind and follow with your heart. Your mind analyzes a situation and come up with the correct course of action and only then does it tell the heart what is the appropriate emotion to feel. We do charitable acts first because we were commanded to, and then we follow with appropriate emotions of brotherly love, pity, compassion...
So the commandment is primary but the intuative feeling is secondary.
Here's more complicated part-
G-d is not a person or a thing- He does not have attributes and we can't define Him. G-d chooses modalities (mercy, kindness, compassion, strength... etc) in which to express Himself to us, and He does request that we immitate them. But He is not bound by them and they do not define Him. It is merely His free choice.
So the mitzvah didn't
have to be kindness or compassion. There is no intrinsic value to it. It could have been anything. It doesn't matter that it's intuitive or feels right or good to us.
It is only the right and good thing to do- simply because He wanted it to be so.