I'm fairly sure the story was called Dinosurs, and its main human character was a very tall humanoid called Drill.
He lived alone on a ship except for a thing made out of sex organs.
He arrives on a world to be terraformed and starts introducing earth lifeforms, such as sharks to the oceans. However the planet is inhabited by a race of civilized reptiles at about the equivalent of 21st century Earth.
They petition Drill to stop the destruction of their world but he says sorry he can't and if they make more trouble soldiers will be dispatched to deal with them. I think they do and the last thing is soldiers arrive in 40mile long ships to kill them all.
I think it was featured on the best science fiction audiotape from like 1995, but I cant find a thing about it anywhere. Does anyone know what it might be?