That's just a tad misleading.
In the first half the Eagles ran 18 times for 69 yards (3.8 ypc) and Hurts had 97 yards passing (13-19, 7.46). In the second half they ran 26 times (79 yds, 3.0 ypc) and threw the ball 6 times (2 comp, 24 yds). They "ran at will" because they had a lead and SF had no QB. In the second half they did have their longest drive of the game (72 yards on 15 plays) but the other 3 drives totaled 31 yards on 18 plays. They played good situational football and the situation was SF had no chance once they fumbled and Philly took a 21-7 lead.
Having said that, yes the niners were the #1 D and Philly didn't fold like a tent. They have a very good team, good on both sides of the ball. I still believe they will need to take a lead and build on it vs KC because if the Chiefs get out to a decent lead, Hurts will have a challenge to bring them back.