Trim - Casing and Baseboard Installation
I would always run the baseboard consistently through a room.

So this suggests that you do something with the window casing. You could rip your window casing and have it touch the base... I don't think that would look terrible. Or (and I'm making assumptions that your window is cased 4 sides like a picture frame, here) you could install a stool/apron at the bottom of the windows and use a much smaller apron to give a bit of room between the base and the window.