I got the (translated) impression that Lefevere was angry (even more than just "annoyed") that Bennett apparently wasn't fully transparent, even while at the same time unable to perform at 100% (which you need to be in a sprint when you're putting unbelievable stress on your knees...). And that Bennett's actions could have possibly aggravated a putatively minor injury.
Given how dominant Bennett has been in the last few years, there's no way he wouldn't take him to the Tour unless he couldn't perform physically.
I hadn't heard of any friction between the two of them, so the whole sequence of events kind of baffled (and disappointed) me.
Still, from a pure publicity standpoint having Cav there, even if he doesn't win a stage, is probably a tossup to having Bennett win multiple stages.