You can file separately without an SSN or ITIN for your spouse, but you cannot file electronically. You would have to mail it in.
You can e-file jointly or separately if your spouse has an ITIN.
Filing separately does not look bad, and is not a factor in audit selection.
Your best bet at this point is to either file separately by mail, or get an ITIN for your spouse, so you can file electronically.
Application for IRS Individual Taxpayer Identification Number
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