Simple. Have the factions on the same map, but have their objectives be different. you still get your csm and the guard still gets to be guard. don't separate faction warfare by maps, instead separate them by objectives. each campaign could have different variations of opponents. maybe the objectives that are important to the guard are not important to the csm, thus the csm fight another faction while the guard fight another.
No ones pretending they'll be playing a Lore accurate Ultramarine ("LULWUT?! NIGHTBRINGER IS MAH BIZZILETITCH!! Made that pansy run away with my Blue armour and chapter name") however one persons can rapidly change the flow of battle, one player plants a melta takes out that tanks rear armour disables the enemies "hammer", kills a couple of people freeing some supressed allies who are then able to use their numbers once out of supression to overwhelm the enemy who were to that point picking off the broken foes. Players won't be broadcast as Uriel Ventris however one player can change the entire flow of a battle especially at such large numbers where even the smallest amount of out numbering a foe can have a real impact provided the enemy aren't space marines who will likely be tremendously numerous and overpowered.
In a fight of hundreds one individual isn't going to make much of a difference. Hell, in games of Team Fortress 2 if you take down one of six guy attacking your capture point this might very well not break their stride. One man is not going to be able to stand against dozens: you need your brothers at your side to stand a chance.
Having deleted 800 words worth of venom on the topic, I elect to sum up my thoughts as: nay to the Imperial Guard. This is to be a contest of titans. They have no place here. Although they could make quite the appealing NPC antagonist faction. I'd gladly build barricades from their dead in a Hordes mode or the like. Put them opposite the tyranids in that role, mayhaps. Damnation; being neutral on the topic is rather more challenging than I expected.
Warriors and Immortals still factually are braindead (or rather, lack any form of free will). If Necrons were to be playable, PCs could only choose from Elite Infantry that far surpasses regular Space Marines, CSMs, Aspect Warriors and Nobs.
Multiple campaigns. Solved. I wouldn't get too upset if you just miss out on one place. Nothing would stop the developers on another campaign in the same place a little later with different factions.
There will be champions. Some people will rise to incredible heights. This is a given in any skill based game.
And said people will still get headshotted by that pesky sniper. Skill can make you into a very effective killing machine, but even a killing machine may break when taking to much heat.
