If I was GM, I would chat with all players individually about this issue and see what they think. Without that knowledge I'd go:
Miller is consistent, has the better contract, but his NMC is already in effect. If Pettersson is dealt, does he just beef with someone else a year from now? His NMC means very limited value. (See: Kesler)
Pettersson is inconsistent, has very low lows, very high highs. Has a BAD contract, but NMC not yet active. Is not a guy who you'd call a leader. No NMC yet, means most value you can get with the extension that is starting.
It's a terrible spot to be for Canucks. But I'd say they'll likely have more success with Miller, who is cheaper as well and right now wouldn't return as much. With that said, I'd move Pettersson.