A number of people have done it. Usually if the Bose amp is getting replaced/bypassed, a new HU is going in as well. Are you sticking with the stock radio, or do you have an aftermarket? From the posts I've seen between here and the OS, none of the people who switched have regretted it or looked back. You may recall on some of the 'audio upgrade' threads, where people wanted to add/upgrade their Bose system, the popular advice is to scrap it and go all aftermarket.
Do you have any particular concerns about the process?