The series has made it clear that illegal aliens are parallels to illegal immigrants, but it’s never made it clear why they aren’t illegal. The aliens, just like illegal immigrants, unlawfully entered the United States and now collect all the benefits of the country without being real citizens. As far as I’m concerned, that’s not “innocent,” no matter how many sad faces they show.
As for the obvious ICE agent stand-ins, the episode decides to offer them a sort of redemption. Brainy (Jesse Rath), a DEO agent and alien himself, later convinces the agents to disobey Lockwood’s orders since it compromises their oath “to defend this country and its constitution.” What’s really compromising the oath is defending foreign intruders, but the plea manages to stir doubt in the other agents.