Yes, you may file a joint return. If you were married on December 31, 2016, this is a legal filing status. The status with the employer only tells them how much tax to take out and does not force you to choose one filing status over another. In fact, many married couples have found that taking taxes out as if they were single helps them on their tax return, especially if they both have income.
More often than not, a joint return produces better benefits than a married filing separate return. Please see this FAQ for more information: https://ttlc.intuit.com/replies/3288477
If you find out that filing joint works out significantly better this year, you may also amend your prior returns for 2013, 2014, and 2015. Here is an FAQ which will direct you to the instructions you would need to do this if it is beneficial to do so: https://ttlc.intuit.com/replies/3288565
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