So practice Shotokan. I've never trained for the Olympics a day in my life.
I don't believe that anyone wants to replace TKD with Shotokan. There is most certainly a difference, even with much older versions of TKD. It was "translated" into Korean, not adopted directly. It was an influence into the creation of the Korean styles, not the sole basis.
Personally, I'm proud of acknowledge the wide range of influences to Korean Martial Arts. They incorporate ideas from both China and Japan to create a unique style. What I personally would love to understand - as many others would as well - is why so many people with so many resources to the contrary simply don't want to admit to any Japanese involvement. Well, either not admit it or just try to brush it under the carpet.