There are no other options.
1. I-539. The advantage of this method is that your spouse need not leave the country to change status, and that once her TD is approved, her current B2 visa will still get her back into US after short visits to Canada/Mexico. The disadvantages are that once she does leave US for anything other than for short visits to Canada or mexico, she will need to get a consular TD visa before re-entering. Also, if she submits I-539 and leaves US before it is approved (and these can take time) then the I-539 was a waste, since she will have to use Consular visa route entirely, as if I-539 was never filed.
2. Consular. Disadvantage, Must leave country and have an appointment. I would go to canada, since she has status there. Advantage is that she controls the process, and once done, it is done and world travel can resume without any worries.