I just think it silly. If I was being generous in my interpretation of the work: The Stormtroopers support an Empire, so analogously it could be seen as a Roman Legionary crucified. Who Crucified Christ? The crowds, the Legionaries, the Sanhedrin? Our sin crucified Christ, so this could be seen as the soldiery having crucified themselves, in a way, in vicarious redemption. It is the sinner borrowing Christ. That we soldiers of the world, we sinners, can still be redeemed. It could actually be construed in a thoughtful, Christian manner.
But the artist said it has nothing to do with religion, so I don't think he put any thought or meaning into it. It is just a situation of importing pop culture into everything. So essentially, it is just dumb. I don't think therefore it deserves any place in an art exhibit, much less one in a church.