nosuperus, from my understanding, you are in a bit of a pickle. Under the ROTP program, they will look at all your marks, high school and post-secondary, but the marks they weigh the most heavily are the 6 most recent courses that you have taken that pertain to the program you intend to join at RMC. So, in short, you can't dismiss your university grades and only apply with high school marks. If you were applying for Sciences in ROTP and took arts in university, they would be forced to weigh your high school science marks, but they will still consider your university marks regardless of the program.
Furthermore, from what I know, the ROTP program will only subsidize students who have more than a year and a half left in a degree program. I may be wrong on that, but I know that if you are in 3rd year, you are cutting it close. That being said, RMC students start at first year. So if you apply to the ROTP program, you likely wouldn't be taken on at RMC because you are halfway through a degree program, and if you were to be accepted into ROTP, you would very likely be placed at a civilian university of your choice, not RMC.
Now, I am not sure how it works if you decide you want to change programs. You may still have a chance at ROTP and to go to RMC if you switch out of arts and into science or engineering, because you would have to start as a first year student that way. I am not certain on this though, and as always, the best source of information on something like this would be your local Canadian Forces Recruiting Centre. You can find the address or phone number of your nearest CFRC on the CF website.