Dropping a little super glue in the holes will still leave some residue in the hole that will grab the screw when you run it in. But, when you take it out again, you're going to tear the wood a bit. Your worry about wearing out the holes by repeated installation/removal of the screws will come to fruition even faster. Because of that, I wouldn't do it.
There are a couple things you could do, if it's gonna make you lose sleep. One, since you don't need as many screws as are installed anyway, you could just bite the heads off a couple screws and superglue them to the pickguard at the positions where you're concerned about the punch-thru. Or, you could get some small threaded inserts, and change all the screws over to machine screws. Then, you could take the pickguard off almost daily without worrying about stripping the holes out.
Or, you could just not worry about it, which would be my choice.