Stats are really a baseball thing where everyone plays everyone else repeatedly, face every pitcher, hitter, etc. They mean so much less in football where you play less than 1/2 the teams in the league.
Is there any disputing that holding the Saints (avg 316) to 200 yards passing is more impressive than holding Oakland (avg 140) to 175? The stats say no.
The defensive numbers this year look better as the schedule hasn't been full of stellar offensive teams - 8 of the 12 games the Pats have played are against teams in the bottom half of the NFL in scoring. The only opponent in the top 10 in scoring to date has been the Jets.
The offense started out at the bottom of the barrel and, while inconsistent, has been improving over the course of time:
17
10
13
30
10
41
23
15
20
31
48
10
This means that the offensive rankings are on the rise, but started from a low point.
The defense, on the other hand, has shown a clear collapse since Thomas went down.
34
28
33
That's an average of over 30ppg since Thomas went down. The question is whether that's causation or correlation. However, before Thomas went down, this defense was actually getting the job done for the most part, so whether it's coincidental or not, it's clear that something impacted the defense.
My personal guess is that the Thomas injury was the proverbial straw breaking the camel's back. An already suspect defense, built with a safety pair that hadn't really worked together and a #2 cornerback who's probably not an NFL quality corner anymore, and stocked with rookies in the very middle of the linebacking corps simply couldn't bounce back from yet another hit.
Hopefully it won't be too late to reverse the problem, and the combination of Thomas, Colvin and (possibly) Seau will settle the front seven and make it easier for the front of the defense to cover for the struggling safeties and inadequate #2 corner (and you can toss inadequate nickel corner into the mix as well).