I've got an example of the legendary Nikkor 105mm f/2.5 with a cluster of marks/scratches on the rear element. I set one of my Nikon bodies up on a good tripod and took shots with the 105mm and my Nikkor 80-200 f/2.8 (itself a stunningly good performer, and this example in excellent condition with no marks or dirt on any element), zoom set so the viewfinder contents were the same as with the 105mm.
Results, even of a detailed scene, were indistinguishable to my eye between the two lenses. Using a D70 body and viewing on the computer at 100% showed a very slight edge in sharpness and contrast in favour of the scratched 105mm.
Don't worry about it!