Take a close look at your ProRes clips and check for interlaced artifacts. My guess is that you're fine, and I wouldn't worry about the other check boxes.
Deinterlace - Don't use it because your 5D footage is not interlaced
Frame Blending - Don't use it, unless you want to change the frame rate of your footage, and even then, MPEG Streamclip probably isn't the best choice for that
Better Downscaling - Only use it if you are converting your footage to a smaller frame size, like 720p or SD
If you are converting 1080 24p H.264 Quicktime files to 1080 24p ProRes Quicktime files, there shouldn't be any scaling involved, so Interlaced scaling wouldn't be triggered (that's just my guess, so take a close look at the footage).
I like to convert through the log and transfer function in FCP 7, but I also recommend Compressor or Droplet for batch conversions. I love MPEG Streamclip too. If you aren't using the batch window, I suggest you do. Also, I like to make presets in MPEG Streamclip, so I don't have to change all my settings every time.
All in all, my bet is that your footage will be fine.