That's blatantly trying to have your cake and eat it. One doesn't get to have a socio-political drama with all the trappings of an allegory for current events and historical strife . . . and get to handwave away any responsibility on the messaging of said allegory by just saying "oh it's all just made up, so it's fine to make out the refugees are secretly the real baddies."
Pick a lane.
There's applicability and metaphor. Applicability is when you can use something to talk about something else, metaphor is when you have something standing in for something else. If the Skrulls are a bunch of racial supremacist people with British accents that used to loot other planets and establish vast dominions over them before collapsing, then you'd be hard pressed to use them as a metaphor for Syria.