Alright, so I went back a few pages and saw a couple posts that touched on this issue, but not to the extent that I generally prefer. So here I'd like to throw out some ideas on how to balance the server/faction/race populations.
It was said by Games Workshop that Space Marines make up about 80% of the sales, so I think we can safely assume Space Marines will be a huge hit in the MMO. Here are my guesses for populations:
Imperium of Man: 70%
Chaos: 15%
Orks: 8%
Eldar: 7%
Now these are of course assuming they don't do any sort of marketing beforehand to try getting people into the right factions. I'm sure Vigil/THQ knows exactly how it will play out if they don't, so I imagine those numbers will even out quite a bit. If we go by how every other W40k game in history has been advertised, however, we'll see 99% Space Marines, 0.9% IoM.

So let's start with the ideas. They don't have to be huge ideas; I imagine the key here will be the little stuff adding up.
Malefactour had the idea to give us a clear representation of the current faction percentages per server before we even enter the game. This will definitely help, but will cause more trouble than it's worth if we don't do something else as well. At near-balance, these percentages will be all the balance necessary, but it'll seem hopeless if a give faction has something like a 15% lead on the others. So knowing more needs to be done, I think this is a given and should be implemented.
Free Faction/Race Transfers: This is slightly difficult to implement, especially if the classes are at all different. If they can do it, then a one-way faction transfer can do a lot to help out the balance. But like the previous idea, this isn't enough to fix the issue.
Faction-Wide Buffs: I'm iffy on this, because in my opinion anything that sets the power level of a given person over that of another should not be implemented. I'm even against something like currency gains due to economies having an effect on the overall power level of a race. So rather than something like a damage or speed increase, they could implement something to increase the race's population faster, such as experience gains (they'll no doubt have levels

). I do think the developers should be striving to avoid giving any buffs at all though.
A more creative option that may not be as viable now as it might have been a few months ago is to place the starter areas and certain hubs closer to advantageous areas. A small amount of resources here, a bit of extra experience there, etc can do a lot to give a race an edge over another, especially if those strategically placed areas give the lower level players of another race a view of how "badass" they are

. This is especially viable if these hubs/strongholds can be moved later on.
Subliminal messages (not really) in the form of cut scenes/pre-rendered videos that appear based on which race needs more players. If the Orks are in trouble, a cut scene for the Orks would appear to make them seem a more viable option than the player may have initially thought. These would appear before the player even made his/her character of course, and they can easily choose any other cutscene they want to view from a cinematics menu. This can be furthered by defaulting the initial character creation process to the lowest populated race.
Now for what I consider to be bad ideas:
Buffs/Tenacity/NPC Help: WoW and other MMOs give buffs based on population imbalances. I personally feel this is a copout and does not fix any of the other issues that come with major population imbalances, such as World PvP, grouping, guilding, and PvP areas where there are enough objectives to spread people too thin. This should be a last resort, as it does not "fix" anything. Additional NPC help is a better option, but still doesn't fix the issues listed.
Faction Lockouts: The idea of stopping someone's character creation due to the actions of other people rubs me the wrong way. This would be a huge turn off to far too many players, because a lot of them just won't play anything but their favorite race. People really get into the IP, and a Space Marine player can truly be
against playing anything else. I feel this idea would be incredibly bad for business as well as PR.
Better Gear/Achievements/Vanity Items: For the same reasons Buffs/Tenacity/NPC Help. It doesn't fix the problem, and can make the other races angry. Picking an underpopulated race shouldn't automatically give you an advantage over everyone else. That just doesn't make sense; it should be a disadvantage.
If it seemed that during this post my opinions of how many factions we'll have leaked through, forgive me. I tried to make it so it would work for any number of factions, including the proposed two.