MS probably isn't happy with the arrangement. But if Destiny shows the direction Bungie would have liked to take Halo (and Reach/ODST kinda show it was)... then I'm glad they're off the franchise personally.
A direction heavily influenced by a new world with its own lore, heavily ambitious. Also heavily influenced by a publisher arrangement (the deal) and a direction heavily influenced by resources split on 4 platforms. If Bungie has shown anything with Destiny it's that they are capable of delivering quality games under a new banner, and to different ships, not just one. Then again I know gamers only look at a metacritic score to gauge success. For Bungie's first endeavor outside MS umbrella, they have done very well in my book. I don't see how Destiny's performance is any indicator of Bungie's performance for a hypothetical Halo Open-world RPG. I have never played Halo 4, I sold my X360 a few months after Halo 3, but I did read some backlash from the hardcore about the linearity of Halo 4. So it's not like 343i re-invented the wheel.