becareful what you read. it is not fine . it is bad. very bad. i've got an '03 wr450, and have had to replace the counter balance shaft twice now. so thats 3 on my bike including factory. the counter balance shaft is what holds, and turns the waterpump impeller.
like you said the inside edges to the c/b shaft do not look square!!!! it SHOULD BE! you need to replace both cb shaft and impeller shaft. it is not cheap. but dude, you need to do more work on your bike. do not ride with the c/b shaft like that, you'll only ruin your new impeller shaft. also, to be honest, i haven't read any others are having problems with this, and would bet almost every wr and wr owner are having the same problem. all do yourself a favor and check the two parts and look for wear. that part is easy, its spend'n all the money to replace everything is hard. like i said, i now have a third cb and impeller shaft combo in a '03 wr450. of course i would like to know why and what causes the problem, but it always looks ok until about a year (season up here) later and......
my only guess is that we are constantly blasting the hell outta the slow guys behind us on the honda
not to slag indy either, but if you have an '03 like me, you might be surprised to find some rounded edges (like your reply, to this guy that maybe has done more damage.) on your cb shaft too.