The puffy cheeks are a very common side effect and will likely start to go away soon.
Personally, I had a fairly bad reaction to Prednisone but that isn't normal. You shouldn't have any long-term effects unless you were to take it for a very long period of time. Short tapers of a steroid are much safer than allowing the disease to run rampant. As is long-term use of Imuran.
Like Cross-stitch said, your doctor should be monitoring you regularly to check for any complications caused by the Imuran. If any are found, the medication would be stopped at the time, before lasting damage is done. Simple as that.
I'm a little worried about treading on your parents' toes here, though. They certainly have a right to have a say in your care, more so than any of us have. I can only tell you what I would do in your situation (or in your parents' situation, if it were my child affected).
I would go off the steroids as directed and stay on the Imuran. I would begin a food journal (if you haven't already), and be as detailed as possible. This allows you to more accurately pinpoint anything causing symptoms (it can be nothing at all, or something as little as a spice, so the journal really helps). I'd certainly hear out the holistic doctor, and perhaps ask for their assistance in creating a diet tailored to my needs. Having an idea of what, if any, foods aggravate your symptoms before creating a diet would be useful. Throughout this, though, I would stay on the Imuran. If in a year or two, all is still well and I simply would feel more comfortable stopping the Imuran, I would stay on the diet while following a GI's instructions for quitting the medication.
Although, honestly, I'd personally prefer to a see a doctor who doesn't blatantly refer to proven medications as "poison." That's a little ignorant and short-sighted. The symptoms and complications of improperly or untreated Crohn's are much more serious than the side effects and complications you
might have from the medications used to treat it.
Either way, I'm confident that everything will be fine as long as you stay under the care of an actual gastroenterologist and keep them well-informed. I hope everyone will keep what you want in mind as they make these decisions.