Unless Apple threatens to remove their music from iTunes if they don't agree to be on Apple Music as a few indie artists have publicly stated.

That point is valid, but Apple is trying to create a de-facto monopoly and even now it's really an oligopoly (which is only marginally better but in many ways worse). In such situations the power balance shifts dramatically and for many artists the choice they have is philosophical at best.

Unless the contract with their label says otherwise.