It really looks like intentional shading, and I think it will be just fine in a quilt. If there are going to be large pieces of this fabric, such as an entire square of it between pieced squares, you might not like the look, but in smaller pieces it will look great. The only way to know is to make a test block, or possibly make a pillow sham to coordinate with the planned quilt. That way you'll be able to wash the completed test piece to see what it does next.