I did a lot of thinking on this one last night.... read through the entire D&D manual "Open Grave" which is all about different kinds of Undead (D&D manuals always make for good research material on this kind of thing).... I still think it would be difficult, but it would be doable.
Essentially you would have to make the Undead have a 0 birth rate. The only way to gain population is to kill things. This would give you Zombie units that can be taken back to a city, and disbanded to become a population unit and Skeleton units which would make for better soliders but could still be turned into populations in a pinch. To get access to more powerful units such as Wights you would have to first create one (from an enemy unit) durring battle (after reasearching the spell). Once you had one, any unit it kills would have a chance of becoming another one.
"Heroes and Chamions" would need to be types such as Liches, and Death Knights.
This would solve the basic issues, but it would still be dificult to balance. On one hand they would be very weak because they have no birth rate, and require acccess to stuff to kill to grow. On the other hand, they could become too strong because they would grow exponentially in each battle they were in.
