Does your trainer want you to stop riding completely or just the number of days or miles you ride? It sounds like your trainer has you on a HIIT program. What is the goal that both of you decided on?
Even though I haven't commuted for a while (Started a new job),when I rode I did it because I enjoyed it. The Cardio or fitness was just a bonus. What is the timetable they gave you for your body to no longer be used to it? When does your trainer plan on changing up the program they started you on so you don't get used to it and keep making progress?
Making drastic changes is hard. Most trainers that I know try to work with or around what you currently do to make it more of a lifestyle choice. If you eat cheesecake everyday (Yum!), then I would suggest only 3-4 times a week to start and then gradually down to 1-2 times a week.