Teams get better and worse throughout the season. That's why you can't just point to games all through the season and apply their results to right now.
After PSU beat Ohio State, Ohio State was still ranked higher than Penn State, and I was ok with that. At that point, it was still quite possible that Penn State's win over OSU was an "any given saturday" kinda thing, and Ohio State was generally better than Penn State (just not on that night).
However, as time has passed since then, Penn State has shown that the outcome of the game that night probably wasn't just an "any given saturday" kinda thing -- Especially when you factor in that their two losses prior to that night were while they were decimated with injuries at the LB position (playing walk-on back ups of walk-on back ups).
Then, again using the OP's scenario, Penn State adds another win vs a top-10 opponent, further solidifying that OSU and PSU are approximate equals.
AT THAT POINT, once it's established that OSU and PSU are approximate equals, the PSU win over OSU makes it illogical to conclude that Ohio State is better than Penn State.