This discussion has spilled over onto bluke's place as well. Check out:
The Jewish Worker: Not Answering 'Amen' to the Second Bracha of Shema: Explaining the Mishna Berura
The discussion here is incomplete without it.
I'm ready to admit that the first answer in the Beit Yosef maintains that Rambam and R' Yonah (who cites Ramban and Ramah as being in agreement) would advocate not saying 'amen' even to the Sha"tz's ha-bocher.
Nevertheless, I think I've demonstrated conclusively that the Beit Yosef's second answer is a more accurate prtrayal of that group of Rishonim.
This has been a lot of fun. Amazing that I can post a 'chaburah', for all intents and purposes, and that it'll actually generate discussion.