In fact I'm pleased to say that I hate the depiction of the Children of Liberty being treated as heroes and one of my first changes would be how angry and hated Ben Lockwood would be. At least post Agent Liberty revelation.
We did see both sides of the public reaction. The anti-alien side was focused on because stories are driven by problems and dangers, but we also saw pro-alien protestors standing against them, we saw the pro-alien march and the events that shifted public opinion more positively, etc.
Making Ben Lockwood head of Homeland Security was insane
No more insane than a lot of the current administration postings in real life. It's only a few steps from what ICE is doing to immigrants right now to what Ben Lockwood was doing in the show.
The point of cautionary tales in speculative fiction is to go further than things have already gone, to warn us how much worse they can get. Back in 2014, Pocket Books published a Star Trek novel miniseries called The Fall, in which a corrupt president took over and tried to turn the Federation and Starfleet down a darker path, and I found it unbelievable at the time how quickly and effectively he managed to take power and shift the Federation's democracy in a more authoritarian direction, especially given that he turned out to be a fraud complicit in the crimes that made it possible for him to seize power. Two years later, I realized it had been prophetic. Sometimes, what seems insane and impossible in the present ends up becoming reality surprisingly quickly.
I had this basic argument on TVtropes.org where it was talked about how dangerous it was that racism was depicted as a thing only "boo hiss" villains should practice because it ignores its affect in systems as well as causal day to day progress. The thing is, where I'm from, it is not actually something that is condemned at all. There are many people who openly state that the Confederacy was an innocent victim, slavery was a benevolent institution with no abuse, and that violence is a logical solution to white genocide.
Bluntly, we need people to villainize racists when they act like villains because otherwise people will assume it's normal.
Frankly, if people are already that far gone, then no work of fiction is going to change their minds. Hell, people like that probably aren't going to be watching Supergirl to begin with, or much of anything on The CW. The targets are the people who are still subject to being swayed, particularly younger people not yet set in their views.
And again, telling good stories with well-drawn characters comes first. It is misunderstanding fiction to think that political messages are its exclusive priority.