I was a controller at IWA up until 2006. Unfortunately, for you the GAP departure is included in an LOA with your flight school. The flight school is responsible for your expertise on these procedures prior to you flying for the school at the airport. The school signed off on it, so it is binding.
The reason for it is that there are more than one tower controller at IWA. The east side controller owns runway 30C and 30R. They also own the west side of the airport above 3000. So when you depart runway 30L to the southeast, or the GAP, the west side controller is working you in their airspace. Since the west side controller only owns up to 3000 they expect you to comply with the procedure which will keep you in their airspace. It is designed to reduce the amount of phraseology the controller has to tell you, and more importantly keep you in his airspace. An airspace violation is usually an automatic pilot deviation. The guys at IWA are usually pretty good about giving you a stern warning on moving on. Maybe there were other factors.
Hope this helps shed some light on the situation.
I'm willing to bet they didn't file anything. It is a tool to inform the flying public of procedures at the airport. It is in no way standard practice at IWA to file a pilot deviation on every single situation. The whole point is to make you aware of things. You need to call Greg, the tower manager, and ask him about it. Don't be aggressive and I assure you nothing will come of this. It's mostly a scare tactic or a genuine informational tool that controllers use. Maybe its a jerk thing to do. Not sure. But, again the whole goal is to inform the public and if scaring them with a pilot deviation meets the goal then there you go. Hey, did they actually take your pilots license number and date of birth?? If not, then definitely don't worry about it. The guys left at IWA tower are pretty top notch in my opinion. They always give the pilot the benefit of the doubt.