Facebook may not be a person, but there are people within Facebook who absolutely can and would be held personally liable for refusing to comply with a warrant, up to and including going to jail.
That Facebook Messenger isn't E2E encrypted definitely is something that can and should be criticized, and they could absolutely do a lot more to educate users on how safe their information is or isn't. On the flip-side, to their credit, WhatsApp is, by default, E2E encrypted. I'd honestly be curious how much value they really get out of Messenger not being encrypted, since if it's really that high, the value from WhatsApp would be significantly higher.
I'm not saying that this is the only reason - because I'm sure they do get some financial value out of it as well - but if you wanted to be charitable, you could say that users generally expect Facebook Messenger to be equally available across devices with full message history, which isn't really feasible when you're signing messages with device-specific keys.