I would suggest just tying them up real tight and champing through the pain for a week or 2.
By then the leather will have sorted itself out and that pinch wont be there anymore.
This has happened to me with my both 11" lace ups with how the tongue was forced to fold when i laced them all the way up. They pinched pretty badly but eventually the leather is forced to flatten out and soften, so to speak. This will happen with yours too, I wouldn't alter the tongue.
you were right Elbron21, i'm glad you talked me into toughing it out, they feel just fine and i didn't have to butcher them. sometimes i'm just a sissy