I have every Mophie Juice Pack available and none of them come over the front glass at all. They rest on the edge of the glass on the plastic borders.
The only way you are destroying your SP is if 1) it isn't put on straight or 2) you are not sliding the case on straight, but at an angle.
In the case of the Air with the snap on back cover, you just have to put the button side on first, line it up and snap it on. That one doesn't touch the front either.
I have no clue how you could be ruining the SP.