Why not, if she doesn't have a physical form why not redesign her voice and 'body' to be a male should she ever be rebuilt. Get a bromance thing going on with Master Chief.
Edit: Didn't expect this to get bumped. Still a rousing topic, should be discussed.
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That would the perfect ending for Halo 4. "Cortana No!" "Chief there's one thing I want to tell you" "What!" "......I'm a man" Cortana dies, chief just sits there for a good solid 45 minutes and walks away