I mentioned the same thing a while ago in the Shanahan thread, but I'm glad you brought this up and quoted the Yahoo article. It makes me feel like I'm not the only conspiracy theorist here
About drafting Maroney...I don't think Belichick thought about it at the time - he was probably going for best value and fit for the Patriots.
However, I LOVE that Polian's plan backfired on him. He resigned all of his receivers and quarterback to huge contracts, and let the engine of his offense sign with Arizona. He was probably eyeing Maroney or Williams to replace Edge. Instead, he's stuck with a slightly better version of Kevin Faulk.
I'll say this: the Colts' golden years have already peaked. Their past two years were their best chance at a championship. From here on out, it will be a slow decline for the rest of Manning's career.