You have a number of options: 1. Quit 2. Do an excellent job, and try and present an unbiased case. 3. Try and present as negative case as possible for IP, a

You have a number of options: 1. Quit 2. Do an excellent job, and try and present an unbiased case. 3. Try and present as negative case as possible for IP, and as positive a case for not protecting the company IP. 4. Don't do it and hope they forget. I doubt they will listen. Limiting your options to quiting or hoping they'll forget. Personally, I'd probably say you don't think that the code can effective be protected by patents but you're not an expert and they may want to find an outside consultant. Then find a new job that better aligns with your interests.