It wasn't the first 96 games, it was 58 before he started producing at an elite level for 104, but he was already making progress just after April (.706 OPS in May).
And it's not like the Phillies would have had a better line-up any day that Nick had sat. Rojas was already playing (and playing mediocre defense in addition to not hitting at the time), Pache is just a mirror image of Nick (bat so bad his defense doesn't justify playing him) and Merrifield was also worse.
Obviously I am joking about it being brilliant managing, but it is the managing style that has worked for Rob Thomson, the winningest manager (by %) in Phillies history). Nick wasn't demanding he play 162 games, it was something Thomson said to several guys as a motivational play, and then it took on a life of its own - and by the time he might have needed a rest, he was thriving, and all of the other big bats were hurt at various times. People always say a slumping guy needs to sit to "clear his head" or for punishment but there's no empirical evidence that works better than playing through it.