Please clarify - With the Sharpshooter In The Tower action used by the Defender you can kill Invader units that are placed behind Cover? By defintion it say any unit on the board while Cover protects from all Marksmen fire.
Sharpshooter in the Tower is not a "marksman" action. Cover doesn't protect units from this.
Since this is something gained from the Cathedral, think of it as holy intervention.