Well, I don't know much about the nuts and bolts of the whole thing. It is true that NPOs file tax returns to the IRS, and it's true that an organization can lose their exempt status by operating as a political organization, and I have heard the rumblings about their involvement in getting CA Prop 8 passed, but I don't know if the line can fully be drawn. I'm not sure how the whole thing was funded (like I said the innerworkings of their support) and I imagine they were smart enough to not directly use the funds, or even in the way that you are saying as distributions that ended up funding the campaign.
Also, depending on the findings it would be a really crazy case. That is one big organization to suspend or revoke, but a very bad precedent to set by letting it go unpunished. Personally, I would hope that the government would drop the hammer on them to set the precedent that we as a nation take those rules seriously. We should take those rules seriously. I can't speak to the reality of the situation though. I just don't know enough about how it all happened or the procedures of the IRS, or if it would be an issue for the FEC or some other governmental organization. I imagine that there is another body who audits these organizations, perhaps one that is more in the direct charge of policing NPO activities (though I'm just guessing, the IRS seems to be the body that would have jurisdiction over exemption status, but it's an awfully big government and the IRS already has a lot on it's plate).