(My situation is identical to yours - I got my GC in July 2007 and filed for my wife in 2007. EB3 India)
See identical thread I had raised a while ago
http://forums.immigration.com/showthread.php?546847-Deep-Experts-question-What-happens-to-dependent-on-I-485-if-primary-acquires-USC
I tend to agree with BigJoe's assessment and discussed with my attorney at length on this
This is no big mystery - file for your N-400, and after getting a naturalization certificate , file an I-130 and send a cover letter to USCIS asking them to amend the spouse's I-485 as that of USC.
The doubts are natural to have and so is fear. But you gotta move on and make the right call for yourself.
I have filed my N-400 and will update this thread again, after I file my spouse's amended I-485.
NOTE - I am not an attorney so my opinion is not LEGAL advice
. Consider getting professional paid legal advice.