It should be able to handle it all right, however realize by default the difference between highest and lowest point is huge, a lot more than you could possibly need to use.  You may want to bring them a bit closer together and just raise the water level.

Yes the difference is huge indeed .  Makes for some pretty cool vantage points.  The map started out as a gimmick for me to fly my a-wing through the canyon pass and has been evolving since.

The idea would be to work your way up from a beach landing to the main imperial base on the plateau through a succession of CPs and increasingly elevated terrain.  The gamemode would be like the Endor Strike Team map.  Linked CPs that cannot be recaptured.  Some CPs can only be accessed by crossing the river canyon using bridges, crazy speeder-bike drivers or air troop transport (if/when they are added).

My title is misleading, sorry.  My concern isn't the heightmap itself.  It is that by lifting and lowering the terrain in this manner creates a whole new (vertical) plain.  With the cliff walls running the length of the map along with the walls of the river I was thinking that there might be problems processing and rendering all this extra real estate.

But if the terrain appearance won't impact performance I should be alright.

You're not rendering a new vertical plane.  You're rendering terrain that is always there, just in a different position.  It wont make a difference, but I can't imagine it will look good, especially with the textures stretched out across it.