Can an orienteering compass be used in place of a protractor?
From your description you are using the orienteering compass to measure course lines by aligning the side of the compass to the grid lines and using the dial to align with the course. There's no thing inherently wrong with this method, if done properly it will give you an accurate course. Personally I like the protractor better, but it is personal choice. You may have to explain what you're doing to an examiner later, I wouldn't imagine it would be disqualifying though, although you never know, some examiners are sticklers for that kind of thing. 

However, before you throw away the protractor I suggest you put one hand behind your back and try to use your orienteering compass to measure a course. You see, at least in the UK you will be tested on your ability to divert, measuring a course using a map while also flying the airplane. That's where that kind of protractor comes into its own, and why I'd recommend you stick with it.