As far as my thoughts go towards starting a campaign. I would say that making up a map of the planet is a good way to start. Even if you don't want to shell out the $50 for Planetary Empires (I know I don't), I'd say take a look at the product page on
GW.
http://www.games-workshop.com/gws/catalog/productDetail.jsp?catId=cat180002a&prodId=prod50017a
It gives you a nice breakdown of the various tiles that are in the box. These can give you a good idea as to what sorts of key structures you want to place across your planet for central objectives of the war as well as give you a starting point to think about what bonuses they could confer to your army. I'm thinking things like no building heavy support units without a manufactorum.
As far as total points for the armies go I would either go with Ringarin's idea of having a massive point value overall list with attrition, or limit the total number of points a faction could have across the planet based on the structures they control with a smaller overall value but allowing for reinforcements.
My personal method for handling the death of named characters would go like this. The first time they are removed from the table in a battle you roll a
d6: roll a 1 and the character dies. If they get taken out again then they die on a 1 or a 2, then a 1-3, etc. It lets them stick around and be heroic but there is still that risk involved.
I like the idea of having the commanders move around on the map and would personally take it a step farther. I would make it so that your army can divide up into forces with set army lists that move across the map.
As far as the added complexity of things like the multi-objective battles around hive cities and the assassination of enemy commanders they do sound interesting, but the main thing you need to keep in mind is just what everyone involved in the campaign wants to do. Ask them what they think of those mission ideas and if they seem interested then work on hammering out any special rules. Battle missions and Planetstrike could be invaluable for this sort of stuff.