I think I understand where you're coming from here - you want the game to run in windowed mode, but cover the entire screen, at a resolution lower than what you normally run Windows at.
If this were possible, it would have to be a feature of the game or your graphics driver. I've checked all of my graphics drivers on various systems and not really seen this as an option. I don't own BF3 on PC (however, I played the beta), but I've not seen this as a game option anywhere previously either. The closest I've seen is using -window -noborder on Source engine games, which isn't exactly the same.
There is a similar option in Modern Warfare 3:
If you are choosing the "Extra" option, Modern Warfare 3 scales up a low resolution (maybe 1024x600 pixels, because that is the rendering resolution used in Modern Warfare 3 for consoles) instead that the game uses the given resolution in the video options like 1920x1080 pixels - typical for console gaming.
That said, you might be able to approximate this by changing your Windows desktop resolution before you load the game. Then play the game in windowed mode at the lower desktop resolution.
Alternatively, since the problem with running in your native resolution is that the frame rate is too low, you might consider messing with the settings to see if you can't boost your frame rate by compromising graphical quality.