If I want to shoot RAW+ (say I only want RAW in case I want to do extreme editing), in Lightroom I treat RAW and JPEG separately (or else it only imports RAW). After the import, I sort by filetype, and reject all of the RAW files and hide rejected. Then I go through my standard workflow of rejecting / flagging. If there is one I want to do more editing in and am limited by JPEG, I copy the settings from the JPEG to that file's RAW and keep on going.
RAW is just as easy to use as JPEG in Lightroom and the only reason I still used JPEG was my in-camera NR, colors, and size. Now that my camera supports compressed DNG, its often less than 2x the size of a JPEG, and embedded profiles can be used with DNG making the colors much better. Now that LR3 has much better NR, better RAW demoasiacing, I've started shooting DNG only with import presets, and it's just like JPEG.