In fact, in my case, I don't think the damage was caused by the other stuff in the bag pressing against the laptop. I think it was caused by the laptop pressing against my back (the padded enclosure is at the very back of the bag).
You may very well be right. Do you sometimes wear your backpack with a waist strap securely fastened, in addition to the shoulder straps adjusted for a comfortable fit? Depending on how snugly fitted your pack is, all it would take to apply at least 20-50 pounds of pressure to the center of the MBP's case under those conditions would be for you to lean forward to tie your shoe or pick up a dropped pen, arching your back and pulling the corners of the machine toward you while the curve in your back pushed the center away. You might, of course, do that half a dozen times a week without ever thinking about it at all, but just once could be enough to damage your display.
A backpack seems, intuitively, like the safest way to carry a notebook computer, and it's certainly a convenient way (because it leaves both hands free). But my feeling has always been that a briefcase-style bag (with or without a shoulder strap) is less likely to apply damaging stresses to the machine inside it, even though it needs more attention to prevent it from swinging into things. I carry my MBP in a slim ballistic nylon briefcase that contains a thickly padded sleeve and a 1/8" Masonite panel on each side of the MBP. That leaves little room inside for many other objects, and there are exterior pockets for all the lumpy ones. Nothing goes inside with the MBP except papers and file folders. If I also had to carry stacks of books around, I'd carry them under my arm, the same way I did 40-45 years ago in high school and college.
I doubt that your thin Marware keyboard protector had anything to do with the problem.