Not exactly. Puyol was playing for the first time after a long injury, that's why Pique said he missed him. It was more of a "good to have you back" type of thing, from what I gather. When you put it the way you did, it looks as if Pique told him he missed him in the sense that he needed his guidance in that game.
But yes, Pique definitely needs a kick in the ass to get him to step up, whether it comes from Puyol or Pep. Or now Tito. But Tito doesn't seem to have the balls to pull the kind of stuff Pep did.
Tbf, benching Pique isn't really an option IMO, since Masch isn't a CB and Bartra's too inexperienced (though he should have got more playing time IMO). He's good for his lack of experience but not good enough to start IMO. If Pique were benched at any point in the season, the options for our starting CB pairing would have been:
Puyol (34 years old) and Masch (not a CB)
Masch (not a CB) and Bartra (inexperienced)
Puyol (34 years old) and Bartra (inexperienced)
Like I said, I don't really see how benching Pique is an option.
Also, this is why I think getting 2 CBs is a good idea. One to replace Puyol as the starter and one to provide depth and a legitimate challenge to Pique's starting spot. It'll give Bartra less playing time though...