If Battlefield 3 is anything like EA's other games that come out on Origin, you wont need to manage the game off of Origin. Battlefield 2142, for example, I just downloaded not even a week ago. Uninstalled Origin because I hate it, and launched the game standalone. Only used Origin to download the game. You can even save the installer, just like you were able to with EA's previous download manager.
Sure, I hate that it's not through Steam. But it's just like if you downloaded it before or through Direct2Drive now. Unless you absolutely CARE to launch it through Steam. And if that's the case, can't you launch third party apps through Steam anyways if you have the exe? Pretty sure you can.