Question 1: Yes, you may file a joint return. The fact that your wife is a sole owner of an LLC does not disqualify you from filing a joint return. Generally speaking, a married couple can always elect to file a joint return.
Question 2: TurboTax Self-Employed should be able to do your return. This will be the case if your wife's LLC is a disregarded entity and she qualifies to file the business as a Sole Proprietorship. A Sole Proprietorship files on a Schedule C, which is included in the personal tax return, which may be prepared using TurboTax Self-Employed.
If the LLC is another entity (such as an actual Corporation or an S-Corp election), she would need to use TurboTax Business to file the business' return. But the description you give makes this sound unlikely. You will probably be able to do both the business and personal taxes on one return using TurboTax Self-Employed.
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