I once read a SF story on exactly this theme - the "transporter" didn't actually transport the person's atoms - a scanner mapped the position and movement of each and every atom in the "source passenger's" body [suspension of disbelief - position _and_ motion? Heisenberg be damned!], and at the destination end, they just had bins of various atoms and molecules where they reassembled the passenger at the destination end. The dilemma was, what do you then do with the "source passenger?" Their solution was to drug the passenger unconscious, then at the destination end, revive them and check them out, to make sure it worked, then phone the guy at the source end, say, "OK," and they'd quietly dump the still unconscious "source passenger" into the disintegrator.
There was some controversy (in the story) about when some hot babe got transported, the "source passenger" would get all kind of groped and abused before they threw her away.
This dirty little secret got out, and much drama ensued. ;-)
Cheers! Rich