Applying for Australian citizenship - different names problem

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I think that your best course of action is to make a call to your local Federal MP's office.
Many have staff who deal with migration and citizenship cases quite frequently and all have special access to staff at the Department of Immigration.

+1

I did this when they knocked back my girlfriends fiance (PR) visa. My old mate was an MP, he referred me to my local MP, who got me an appointment with the state director of immigration, who said "i cant see anything wrong with her/your application, let me make an enquiry"
A month later, the overseas embassy invites my lady in for an interview and bingo, rubber stamps it, and before I knew it, I'm married, mortgage, kids, pension plan. 20+ years on, definitely was worth that little bit of effort.

I know thats not the same, but it just gives you a stepping stone to get to speak with someone in immigration that knows when to apply common sense.