The most plausible explanation is that Moody/Crouch wished to continue at Hogwarts as Voldermort’s spy. If Harry disappeared under Moody’s watch, he would be quickly found out. But for Harry to mysteriously go missing in the maze (remember, the Cup would have returned by itself), the blame would not fall on Moody, especially with Krum under the Imperius Curse and ready to take the blame (admittedly, this is all conjecture, but it does appear to make sense).
To add, Voldemort always wanted a spy around Dumbledore. “One of our number has left us forever” makes it sound that he suspected Snape of treachery and of becoming a member of the Order. He would have wanted to replace Snape. However, he could have Imperiused anybody else to present Harry with a Portkey, or even sent it to him for Christmas!
And it’s worth remembering, Crouch was a certified madman.
But whatever Voldemort’s problems were, he wasn’t the certified madman Crouch was. He wouldn’t have let through such a plan.