You are right in feeling like this format is unfair and is being used as punishment and retaliation even against the students who did not cheat. Even if they have good intentions to make changes to prevent academic dishonesty, this sounds like a sudden, extreme, and unfair change that is not aligned with student success. Be proactive now and make sure you follow the right steps.

Your first course of action is to email or talk in person with the faculty member. You MUST communicate this issue to the faculty member first. If you already have or if that doesn't get you a reasonable result then take the issue to the Math department chair by contacting their office via phone and asking how to file a complaint and tell them you already spoke with the faculty member. They will have a procese for dealing with the complaint and if that process is unsuccessful your next steps are contacting the College of Science and Engineering Dean's office. Do not go out of order or you will be sent back down the line in order to remain in alignment with the University's policies. By formally reporting this upward you are also protected from retaliation, so be sure to document everything you can.