Yes, the Pats surrendered 4.9 YPC running light formations that dared teams to run in an effort to make them chew up clock.
If the Pats are behind, their strategy will change. That means less nickel, no more 260 pound Geneo Grissom at DT, and a lot more Branch/Siliga/Hicks on the line. That'll mean having 3 LBs on the field regularly enough to make Mayo more than a bit player in this defense. These are all steps that the Pats can take and will take the moment it becomes imperative to stop the run. We've seen it happen before, and we'll see it happen again. Strategy changes dramatically based on score and time remaining.
It's standard situational football, Belichick lives for this stuff. If a team that we're conceding the run to runs for a bunch of yards, I don't really care. If a team runs for a bunch of yards when we've made stopping the run a priority, then I'll be worried.
The Pats' run defense not only isn't worst-in-the-league, it isn't even bad. The YPC number will go down once the Pats regularly find themselves in situation where they aren't up by 3 TDs and running out the clock.