The color space set in the camera has no effect on RAW files, only in camera Jpegs. So you are correct in that respect and can work on the files in Prophoto without any problems. Just make sure your Raw convertor is set to output your files in Prophoto when it sends them to Photoshop or your external editor.
If you are using ACR to convert just make sure the working space in Photoshop is set to Prophoto and you are good to go.
Thank you Rich. I just wasn't sure. I'll give er a go.