The CPM isn't going to replace the air squats and it will not castrate you. You use it most in the first several days post-op and it helps w/ pain and swelling... scar tissue formation and supposedly w/ speed of healing in the early days also. We're talking about 6+ hours of motion a day in a maybe 20 second cycle. You're not going to do air squats in the first few days anyway as you probably won't be cleared out of your bed w/o a locked knee brace for that long. If anything, using the CPM will get you to your beloved air squats faster.
As to the hamstring graft... why throw away some perfectly good muscles? http://www.ncbi.nlm.nih.gov/pubmed/16226644
(which, ironically, serve to stabilize the knee). You can read on the web that opinions on this vary a lot but i'd go for patellar tendon again or maybe allograft. Allografts have a high failure rate in young athletes etc ... but i find it persuasive (no professional qualification to judge either way) that a significant problem is that people return to action too fast w/ it instead of giving it the year it needs for tissue to grow into the matrix and that that's a significant reason for higher failure rates.
Anyway, this is all covered in other threads and forums so you can read discussions, pros and cons, but it's your leg so don't just put the decision on autopilot.
You'll find that your finely-honed CrossFit instincts will not be useful in this situation. Hundreds of air squats will just fuck things up, like they always do. You're going to have to actually think through this process.
And were it my knee, I'd have the patellar tendon autograft done, again.
Obviously I won't actually do hundreds of air squats... I meant that I would rather do work myself instead of letting a machine do it for me. It's more clear now though, I thought it would be replacing physical work that you would otherwise get during rehab. Veryhrm, my apologies for drawing conclusions too early, and thanks for your valuable insight and help!
I'm getting convinced that the patellar tendon autograft would actually be better, now that I've read some more scientific articles comparing both methods, and more importantly, listened to experts like you. The only downside seems to be some more pain during recovery, but that's no problem.
One thing though Rip, Crossfit-instincts, really? I'm a true believer of Starting Strength... I'm sorry if I offended you by butchering the program in my despair on the first page. Thanks for the help and suggestions, I really appreciate it.