Orton was planning to retire but didn't tell anyone. Marrone was planning to opt out and kept it to himself.
How does the decision to start Orton against the Patriots look in that light? On the one hand, with Orton secretly hanging it up, the Bills might have thought playing him would be an extra look at him before next year's battle for the starting QB position. If the team had known he was done, they might have wanted to give EJ the chance to end the season on a high note like Geno did.
On the other hand, if it was known that Marrone was planning to opt out, might management have instructed him to start EJ? His motivation in starting Orton is now suspect, because the W was more important to him for short term reasons (had a winning record in Buffalo, makes him more interesting to other teams) than for long term reasons (help remove the cloud around the future of the QB position).