firstly, thanks to everyone for their input, I am slowly building a very strong case to take to my CoC regarding this issue. Also, to clarify (and to stop the bashing of sigs hahaha), I am not posted to the sigs regiment here in Kingston. I am in a tri-service unit with a very inexperienced and new CoC (excluding the Maj and my Capt who have significant experience) which might help explain the stupidity of this new policy.
As previously mentioned I am going to pick and choose VERY carefully when and where and how I bring this issue up to avoid (as someone already mentioned) painting a target on my back or making the situation worse. That being said, I will not be releasing any of my medical information to my CoC (if I need to attend the MIR in the near future) seeing as I have TONS of references now explicitly stating they do not have the right to know those things.
After poking at my CoC today regarding the issue, they are now saying that they just need the "basics" about why you are going; whatever that means. To be honest, however, at this point I am now beginning to think they don't have the right to know anything other than "I am sick/injured and will be at the MIR."
Once again thanks for the help from everyone. Army.ca rocks!