Think about it in terms of incentives and scarce resources. If the students know they can come and protest to you with no additional consequences, they will certainly do so, guilty or no. Everyone has heard the story of merciful teachers and cops that don't give a ticket if you cry. At worst, they are out two hours, and at best, they may get a higher grade with very little work. Basically, your time has become a commons whose use has no real cost to the individuals taking advantage of it, but from which they believe some value can be extracted.
The economic solution is to make sure the time costs something, so that the students will consider whether there's really enough utility in protesting to make it worth the cost. The cost is that if they protest, they run the risk of suspension in the event they are actually guilty. It should be obvious to students that this will be the likely outcome if they do protest.
Let me know if I'm reading you wrong because I really am curious if students protested even though any protest would result in an immediate referral to the honor board. Also, thanks for fighting the good fight even though it got you screwed in the end. We need more folks like that.
Oh, I didn't mention the one other advantage this approach has. If you quickly and forcefully deal with students who have violated class policies, I think there will be less emotional "splash damage." It's the same way a parent should not draw out a punishment over a long period of time -- make it hard, get it over with, and wipe the slate clean so you can smile at each other the next day.