I just found this on the official ABC Alias website ... I think it proves that Francie can't be a man...
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Who is Francie's genetic double?
At this point, almost nothing is known about the woman who killed Francie and took her place in Sydney's life. The only thing known for a certainty is that Sloane bankrolled a genetic doubling program and this woman was the second patient. Once the operation was a success, she arrived in Los Angeles, killed Francie and took her place. Her physical likeness is a perfect match, and at this point, Sydney seems unaware of the replacement. However, this new Francie has a different demeanor than the old one — and Syd occasionally finds herself feeling awkward around her "best friend."
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It says, "This woman..." therefore... Evil Francie couldn't be a man... (which I am very glad to hear...)