i remember reading that issue! i find that marvel (particularly in the inhumans series) often tries to insert allegories these days that... don't really work? like, from what i remember of civil war II, it wasnt so much 'morally ambiguous' as 'morally floppy and confusing.' it didnt have the strength of the original civil war's concept and arguments. the whole profiling thing... fell flat. just didnt make sense. i think oppression metaphors, when done right, can be really powerful ways to explore a harrowing issue in a safe and accessible fantasy. done wrong, theyre just... limp at best, insulting at worst. the tv show cleverman is the best example i can conjure for oppression metaphor done well, if youre interested. the x men have also been very strong in this concept at times, particularly in their conception.
as for moral ambiguity - it can be. it depends on the message or theme of the story, what theyre exploring. civil war, the original comic event, explored issues of state surveillance and control. in a fairly neutral way, the event set up the situation, and writers and characters on both sides of the debate got to expand their arguments. im not 100 on it, but its a really interesting way to collaboratively debate an issue through art, and some of their arcs - such as the young avengers & runaways arc, and the xmen involvement - really hit home. the level playing field here allows the issue nuance and full exploration.
on the flipside, harry potter is pretty morally black and white (leaving snape out of the discussion.) the allegories in the series are about white supremacy and fascism - voldemort is wizard hitler (technically grindelwald is, but thats where we get into a discussion of jkr using the allegory poorly). its not a space for ambiguity in the story, because the message has no ambiguity. genocide is bad. racism is bad. theres no other hand there.
ooooooooooooooooooon the other hand, i think sometimes people confuse 'moral ambiguity' with 'having fully fleshed out villains.' no matter what your story and message, having a fully fleshed out villain - whose drive is stronger than evil for evil's sake - makes your story (and therefor argument) stronger and more compelling. not all fleshed out villains have to have redeeming features, i think, but they must believe in what theyre doing, for the greater good. i think series of unfortunate events is a great example of an unambiguously evil villain who is fully fleshed out. [[[spoilers]]] count olaf reveals a tragic side in the final book, whichll prolly be explored more in the tv show, and its understood that he could have been so much better than he is. however, this doesnt redeem him, hes still an evil man. thats just suddenly so much more tragic.
sorry, i think this is a bit rambly, but tl;dr allegories need to be handled carefully to have any kind of impact, let alone the intended impact, and theres a time and a place for ambiguity.