I think I have found a way to make the window bigger that tops all of the solutions you mentioned. It works like this: Start the game, choose 640x480 as window size in the in-game menu, then open your Windows Magnifier app and set it to 200%. You are now playing the game in 1280x960 resolution plus cleartype-sub-pixel anti-aliasing, which is built into the magnifier app since Windows 7.
Should the game still look as bad as with regular 1280x960 resolution, chances are that the cleartype anti-aliasing is turned off in your windows settings. In that case, click on the gearwheel on your magnifier app, go to "settings" and enable "Smooth edges of images and text".