Yeah, the thing with Ernst is he means what he says. He’s a fanatical idealist, and pretty much embodies the ideals that the Federacy is based upon. So if his people were to ever betray said ideals, he’s definitely backing up that claim.
It goes back to the conversation he had with Theo in episode 12. If humanity is willing to sacrifice children in order to win, then humanity might as well die - along the lines of that anyways. And the Federacy is pretty much doing that, despite them being the most suited for it. He pretty much sees them as his ‘children’ at the point, considering he lost his family, as he subtly mentioned near the end of episode 12.