This is the worst part of both campaigns in my opinion, with the well-cave battle being an easy second place. Some tips which have been pointed out in other threads on this topic, and which I've used myself:
Just finished the game myself and i agree that Endurium`s tips are very effective in completing this stage of the game. It took me some reloading to beat the escort mission, but once i actually started using the nuke skill it got alot simpler;)