That's honestly why I do not carry pens in my bags. If I do, I put them inside a cheap accessories bag... I'm so sorry this happened.
I agree and would just have the lining replaced. But you may want to wait and if you decide one day to replace the leather you can do all of it at once! Although it won't be cheap.
You just want to be careful not to get it too wet as you clean it (with whatever method you choose) in order to avoid the blue sinking through to the canvas. That happened to me with a DA speedy.