I think we're talking about two differnt things. You do want to crop all your sprite frames when you're done to save texture space, memory, file-space, load-time etc right?
If so, you dont want this to RUIN half of your image points and collision shapes and ruin your game, right?
Is it me, or does cropping currently ruin the shape of collision polys and image points if they are outside the "safe area" where theres actually image.
About the issue of cropping inside the editor I really said nothing about, I just concerned about avoiding the issues it can make, and it make sense, one time you change the sprite size by cropping it and all the frame points and areas points are relatively to a origin:
Also, your animation points and collision areas can have the same relative origin, making easy "set to all animations" and avoiding bugs with collision masks with different sizes, changing then on the run time, putting your player inside wall, for example.
I workaround these type of issues just editing the images directly, using software like Fireworks, who can do batch processes, and with C2 closed, then opening C2 again.
Sometimes some adjustments are necessary, but it work well.
Best luck and I hope a solution for your problem too.