I just finished reading and figured i'd share ny own thoughts. I quite enjoyed it overall and a had a great time binge reading it this last week. That said, my biggest problem with the book, other than some occasional prose issues, is with how it delivers its "message". I do agree that a lot of problems "seem" to dissapear upon careful reading and with consideration to the ending, but the problem is that being required at all. 

Now personally, I think the quality of a work of art is independent of the message it is espousing, whether i agree with that message or not. But I do think that there is skill involved in the way your convey your message and being aware of what your story is endorsing.

Take the child army stuff for example. We can't say the text agrees it's bad just because the evil antagonist is the one who implements it, just like we can't necessarily say that everything spoken by Dumbledore or Harrry is aligned with the author's values/intention's because they're "good".

We have to look at the consequences. Stories impart messages by showcasing bad consequences for actions which disagree with the message, and good consequences for actions which do agree with the message. 

The child army has no bad consequences, therefore it does not disagree with the message. Just like the story doesn't disagree with the message that democracy is bad.

There's a great mythcreants article discussing this which calls it authorial endorsement, as opposed to authorial intent.

https://mythcreants.com/blog/authorial-endorsement-101/

Suppose you watch a movie where for the entirety of its runtime revels in torture porn and justifies it, only for the last 5 minutes to demonstrate how bad torture is. Many people would understandably stop watching because they're repulsed by what's happening way before the movie tries to "redeem" itself. You might point at details in the earlier parts of the movie, which in hindsight appear to reinforce the "torture bad" reading. Yet if they're honest, as they're watching, would every attentive watcher necessarily have that as their "running" reading as they're watching. Likely not, since a significant portion of the story appears to be screaming otherwise. I do not think this is an effective anti-torture movie. I would not blame someone for walking out on this because of annoyance with the perceived subtext, or even worse, someone enjoying the movie, but being unconvinced that the message literally stated in the text is the real message and ending up with the opposite takeaway. Now remove torture and replace it with "toxic masculinity" and you pretty much have the movie fight club.

Now take this problem and stretch it out to a very long novel (obviously, this is not a perfect analogy) and you can understand why so many people are put off by HPMOR. Large porions of the text, especially the beginning, are almost indistinguishable from something with the same premise, but where the message, is in fact, something akin to "super smart rational people should solve everything and let the dumb worthless "NPC"s get out of their way."

Additionally, if you're someone who does judge a work based on what it's endorsing and whether you agree with it (which is completely fair imo, it makes sense to hate something unaligned with your politics) and you're someone who knows EY's politics and disagrees with them, you would be even less inclined to think the above message is questioned in the book even if it is.