There may be someone else on the forum who is more knowledgeable than I am but we were in a similar situation last year and my understanding is that your employer(s) are already preparing and calculating tax due as a married couple so your tax credits will be taken into account for both of you.
What you will want to do is request a balancing statement from Revenue at the start of 2013 for the 2012 tax year (since I am guessing she will begin mat leave in 2012?) and then again in 2014 for the tax year 2013 to make sure any differences in the tax credits are taken into account. Hopefully this will result in an adjustment in your favour! You might want to ensure your (and her) employer is calculating your tax based on a married assessment.