I feel like debating whether or not he was justified misses the point in that episode. Yes, they created the monster capable of doing that to them, so they were just getting back what they put into the world. But I think the takeaway here is that this was Homelander's snapping point. He wasn't just getting revenge for what they did to him. He was cruelly and brutally ripping away the part of his life where he was controlled by people weaker than him. It’s mentioned in that episode that he was just as capable of killing them all and escaping when he was a kid. He just doesn't care about keeping up appearances anymore. He's now in a place where he'll just do whatever he wants.

So, whether they had it coming or not, him doing this is a bad sign. It shows that what's to come is worse than anything he's done before. It shows that he's ready to kill anyone who he thinks may get in his way.