I am fine with art-flipping, like occurs in Planetfall; when infantry units move onto coastal tiles, they change art into a naval transport unit. Here, when fremen move onto the desert they convert to a worm rider tile. Ideally though if there are multiple units that do this, they need to have slightly different worm-rider graphics.
I am also fine with the idea of having some Worm units as desert only transports, buildable only in coastal cities.
I do not understand why you have a problem to this; you can have Worms buildable only in coastal cities for the same reason that you can build ships only in coastal cities in vanilla.
Worms live in the desert, they really don't like going on rock, and won't do so over any significant distance. So you can't recruit worms away from the desert; there aren't any worms there to recruit.
The scene from the David Lynch movie of worms attacking the city is horribly uncanon. In the book they just use worms as transport in the desert to get near the city. They blow open the shield wall to let the storm in, and then attack as infantry.
The main argument was also about barbarian sandworms being able to enter non-desert tiles. There was one patch where you fixed the barbarian worms not being able to enter cultural borders, but still had them able to enter land tiles, and this was truly horrible. Worms would just walk around your empire killing your stuff, stopping you from building imrpovements and pillaging. That was no fun to play at all.
It also seems like building worms in coastal only cities is possible, if we decide to go that way, despite having removed the idea of a "coastal city" from the mod:
http://forums.civfanatics.com/showthread.php?t=332066&page=2
Take a look at posts 31 and 34.
It turns out that it is possible to have buildings that are not buildable in landlocked cities (discovered by accident through bug). So it would be a simple matter to have desert-only units require such a building, and to have this building be very cheap.