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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Dude, come on. Don't be so inconsiderate. Cortana [b][i]is[/i][/b] a man. [spoiler]A big beefy man with holographic yeti hands.[/spoiler]