Yes, you can claim your Foreign Earned Income Exclusion on a Joint return, even if your spouse was in the United States for more than 30 days during that period. Her Residence does not affect your Exclusion.
As a side note, does your spouse earn income outside of the US? Without knowing the specifics of your situation, it is still possible that you spouse would qualify for the Foreign Earned Income Exclusion on her Foreign Income. For example, if she was outside of the US for July 2015-June 2016 (or August 2016-July 2017), she could exclude and foreign earned income from that period.
