I wouldn't call 24 carries for 99 yards as being "shut down". Maybe relative to his previous efforts against the Packers and his 2012 season averages, but for most RBs that's a damn good day against 7 man fronts. Peterson put up those numbers against massively stacked boxes all damn day while Joe Webb made dookie on the field.
However, I also don't think he's an argument for comeback player of the year. He played 12 games last season. Manning played zero. Peterson had a serious injury, but it's one a dozen players or more come back from every year. Manning's was an unprecedented injury with serious career risk, at an age when most guys are already hanging it up anyhow. To me comeback player isn't even a tough choice at all.
Back to MVP though, I personally want to see Peterson win it. Manning had an excellent season but the Broncos were an 8-8 team with Tebow at QB, a less developed Thomas, Decker, etc., worse OL play, and a far worse defense last year. Manning took this team from "solid and getting better" to "elite". Peterson's season this year took the Vikings from a 3-13 team to a 10-6 team. That would be insane improvement for a QB, it's even more impressive coming from a running back.
Manning had a damn good season, one of his personal best. Peterson had what might have been the best running back season of all time (32 less carries than Dickerson with 9 yards less rushing, 6.0 YPC, most yards after contact ever, ran against 8 and 9 man boxes all season long). If you don't give it to Peterson you might as well just admit that it's a QB only award from here on out, because no one is putting up a better argument for the award than Peterson did this year. Meanwhile Manning and Brady are working in a passing inflated league while Peterson is facing exactly the opposite.