i don't think this is eheim's problem. as far as i can see they were very respectful to you, a person emailing them out of the blue wanting discounted stuff because you didn't read the box or research the product first. they upgraded their package, now everything is included. should they turn around and send free sets of media and new parts to everyone with an older model?
this should have been between you and the LFS owner. eheim made the product but they don't set the retail prices. it's the LFS owner's fault/problem/scam/mistake that he's selling two different products for the same price. i don't see how returning a product is "rude for everyone involved". At most it was a mistaken purchase - you did not get what you were expecting. That's what return policies are FOR. Maybe the LFS owner was totally ignorant that the products were different, but instead of keeping it a big secret, maybe he should be informed of that fact so this doesn't happen in the future?
Is the owner an ex-Mafia bruiser or something? "I know the owner so don't tell him! I really don't want to talk to the dealer about this..." It just sounds really weird, and sort of like a scam - you have the solution right in front of you, but refuse to do it that way.