You didn't list the prices you found, but from your post:
There is almost 7k savings going through ICN vs direct to Tokyo
So it implies the nonstop ticket is 3500 more expensive than the 1-stop flight.
But...
On momondo I found a 1-stop AC/OZ itinerary for 3400ish per ticket.
There is a non-stop JL flight for 3700ish per ticket.
And if you want to stick with Star Alliance, NH can do it for 3900.
A nonstop AC flight is listed at 4200.
So maybe give momondo a spin?