I like the idea of having the shortcut, but also having some benefit to not taking such a shortcut.
Like, say, having a reward granted to the PC if they can take out Bugs without teleporting, digging, or reading scrolls of vermin control. Perhaps their god can go "YOU HAVE IMPRESSED ME WITH YOUR HONOUR AND PATIENCE, MORTAL!" and a random artifact could materialise at the PC's feet. Or something along those lines.
On the more general topic of the request, I do like the idea of adjusting the order of the levels. But I also wonder about the positioning of the shortcut - it's supposed to provide a bypass route for early levels, but if placed above or below certain levels, it changes the requirements for movement. For instance, if the shortcut is below the EG, then the PC only needs to get past it once, and then they can use the shortcut from then on, whereas if the shortcut is above the EG, then moving back and forth means dealing with the EG every time (I'm assuming, here, that the PC isn't wearing the RotHK).
Similarly, if the shortcut is below the Wall of Flames, then the PC has to get the orb before being given access to the shortcut, whereas if it's above the Wall, the PC can use the shortcut, go to the tower, and use the shortcut again to get to the wall and pass it. Thus, these issues need to be considered.
One option could be to introduce a second shortcut, and move the first shortcut up to, say, just below the Water Temple. The second shortcut could perhaps lead back to an earlier level of the CoC... and be placed on the Bunny level, on the far side... and only appearing if the PC kills Bugs without a shortcut. The god could grant the PC access to a "divine shortcut" for their patience. This way, the player gets to decide between the challenge of dealing with the Bunnies and the challenge of dealing with traversals up and down the CoC.