Since your wife pays taxes to Canada, you could use the foreign tax credit rather than the foreign income exclusion to report her income. This allows for credits that he use of the foreign earned income exclusion does not. However, if your wife has used the foreign earned income exclusion in prior years, then not taking it this year constitutes "revoking" it, and she will not be able to take the exclusion for 5 years (without permission from the IRS which is expensive to request and not guaranteed to be granted.)
You cannot exclude only part of her income unless her income exceeds the exclusion allowance.
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