It's an interesting question and I guess it would depend on the circumstances.
If, let's say, a battle had been raging all season between VR, JL and DP, they were within 25 pts or a DNF with 4 races to go..would you expect team orders to be issued? When are they implemented if indeed they are?
Remember Dani torpedoing Nick in Portugal 2006? He was 34 pts behind his team mate going into the 2nd to last round there, lying 5th in the standings. Hayden was leading with a fast closing Rossi 2nd just 12 pts back. If Rossi hadn't fallen at the final round handing back the advantage by 5 pts, Dani's move would have cost Nicky and Honda the title. Clearly no team orders there.
If Rossi was so far behind Jorge/Dani he couldn't win the title and he was able, you'd expect him to ride for his team mate and the factory.
I don't think any of us like the idea of team orders which implies a fix, because we want flat out honest action. However, you'd have to be naive to maintain there is no scenario when they can come into play.
If you think Rossi would come 2nd to Jorge when he can still mathematically win a title himself because Lorenzo is supposedly #1 and Yamaha wish it..I think you're dreaming.