Personally, I don't have a problem with the message. I think the El's view us as lesser, backwards people and someone from their society can improve and advance us to be more Krypton like, and for their son to keep the kryptonian blood line alive.
But it'll probably be revealed it was a bad translation to make it come off as nefarious.
You get it,only thing wrong with the message is that its coming from a alien and it got out publically.
Taking many wives? Only evil in Babylon but perfectly normal in many cultures to carry on your legacy.
Lord over the earth and guide humans? How is a Superman who has umcomprimising morals lording over the earth a bad thing

?
All Clark hears in the message was kill people because
a)he good to such a fault its a weakness and he doesnt believe in killing anybody
B) hes xenophobic and sees polygamy thats practiced in many cultures as weird due to his American programming. Still believes in fake american values like "democracy".
Like i said,the message doesnt need to be retconned because the position the kryptone are coming from is same grey area that America and other superpowers operate in. For whatever reason people think Clarks parents would assume he would be evil,or raised to where he would become a homicidal tyrant and rapist. Maybe they assumed he would be raised right,and actually end up a good and gracious king
The reactions to the the message really is just highlighting peoples xenophobia

#MESSAGE