I love Signal, and I have persuaded people to use it a lot. That said, it is definitely not the gold standard for privacy. It's a good-enough compromise between actual unbreakable encryption and trivial for anyone to use. It's always been valuable for that reason, and still is.
Don't worry about Molly - it uses a variation of the same code that Signal does, so they don't need "help" to get critical fixes that Signal receives. Use it if you like it!
The actual gold standard for privacy would be logging in through TOR and sending GPG-encrypted messages that way. And there's an app which does this, too - it's called Briar. (No phone number needed, either!) It's not as seamless to set up as Signal is, though.