When I first started inking in OneNote, my initial response to erasing with the Surface Pen was "Bummer!" I thought it was going to respond like a more traditional erasing experience. Instead, an entire line, letter, stroke, etc. would disappear.
To my understanding, this is the default eraser setting in OneNote. Like many other settings with the application, it is customizable. If you want your eraser actions to erase only where your pen touches, simply go to DRAW > Eraser and then select the size of eraser mark you want.
Now, the only thing that gets erased on your page is precisely what the tip of your Pen--or the cursor box if using a mouse--touches. This is easily changed if you ever want a bigger or smaller eraser mark, or if you want to go back to erasing an entire pen stroke.