The option to Include Spouse is based on the Spouse Relationship regardless of if the Spouse is marked as Deceased.

The relationship can be changed to a non-spouse relationship by navigating to the Relationship tab, opening the spouse relationship and unchecking the Spouse button in the lower left corner of the relationship and click Save and Close on the relationship record.  This will keep the relationship record with the Constituent, but it will no longer be a spouse relationship.