The FTC authorized the merger as long as some terms in a consent degree were followed by both parties. It's very possible that the FTC just said "yeah, whatever the Pentagon wants" and waved it through. But to be honest, I'm not sure if keeping the two companies separate would have been any more efficient. It's already a duopoly with a single, captive buyer, and there's no way that one provider is going to charge much less than the other guy. It's like the airlines. One company set its rates on Monday, and on Tuesday, everyone else sets the same rates.
It also sounds like Boeing and Lockheed Martin was suing their crap out of each other before joining the ULA. If you look at the KC-X program to provide an aeriel refueling plane to succeed the KC-135, lawsuits can keep a program from going forward for years. The Air Force/Pentagon/Boeing/Lockheed/FTC might have just looked at all this horseshit, and said, screw it.