If it checks out every other way I would be tempted to call Canon send it and have the front element replaced.
One thing to keep in mind though is that under the Canon warranty they do not have to send you the same lens back, and you may end up with another copy.

My concern would be sunsets and your long exposure waterfalls. I think if it was going to be noticeable it would be then.

Another consideration is resell. If I were buying a lens and looked it over and saw this I might pass on it.