What the heck do I know about Dune? I only saw the movie (haven't read the book so I have nothing but that distant, very faded memory to go on). All I clearly remember is the huge worms coming out of the sand, to be honest...hence the focus of my suggestions.
I can definitely help with scenario mechanics though:
If you're using ToT, you could also add a second 'subterranian' map with transport tiles all over it linking to transport tiles on the main map (only on sand tiles) and give only worm units the ability to use transport sites. That way, you could have worms popping up when you least expect them to.
An alternative is to randomly spawn worms all over the map and set the 'destroyed after attacking' flag for that unit type (this is so that you don't get a multiplier effect--more worms each time a new one appears). That way, you get a similar effect without having to use another map--just don't set too low a value for the 'denominator=' parameter in the 'RandomTurn' trigger or you will probably have too many worm units popping up and Dune will be overrun with worms...except for rocky tiles. The advantage of doing it this way is that you can use Civ2:MGE, but you won't have the impassable terrain. In MGE, the only way I can think to stop the worms from entering rocky tiles is to surround the rocky tiles with immobile air units belonging to your civ, thus your units can go in and out but the worms can't (they can't attack air units). The problem then is that other civs can't enter the rocky terrain either. Other than that, I can't think of another alternative except maybe some clever use of Ocean terrain making it look like land and giving your civ all heli air units or something...but then you'd have the loss of health problem for air units with 0-fuel, which is overcome only in ToT...well, that was pointless.
Another alternative: if using ToT, you could use the 'Delay' modifier with the 'UnitKilled' trigger to spawn (CreatUnit action) a worm x # of turns after a worm is destroyed. This will ensure that the worm population is not eliminated by an ambitious player, while keeping the worm population the same but not re-spawning them immediately--just remember to populate Dune with x # of worms from the start otherwise this event will be pointless.
(I'm giving you options so that you can use the one--if any--that best suits the needs of your scen.)
BTW, in these examples I'm assuming you're going to use the Barbarian--8th--civ for Dune's wildlife.
Does Dune have changing weather patterns or is it always...uh...Dune-ish? If the former, you can use a batch file to change the terrain (or any other files; e.g. Rules.txt) to match the weather.
The more info on Dune you post, the more civ-equivilants I can post.