Unfortunately, because of the way the data\text\ files are implemented by CA, the only way to do this is to have seperate installs for each campaign. You might want to check out the TFT mod (see my sig) for an idea of how we worked around multiple campaigns. We didn't specifically have more factions, but other stuff is different across each campaign.
Basically, we have a base mod with common files (the bulk of our download) and then seperate installers for each campaign.
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