Well, I think we're forgetting several main details in the Norris and the Warrant plotline...
1. Player Characters are intimately involved with retrieving the Warrant in CT Adv 1: Kinunir
2. Let's not forget the pretty dire hazards involved in getting it... namely a rogue AI and an asteroid belt full of loose antimatter.
3. The CT supplement/adventure The Spinward Marches Campaign briefly discusses the risks to Norris and his house if his gambit had failed. Because GDW's writing style was pretty minimalist at that time, you have extrapolate just what might have happened if Norris' coup had not worked in several different scenarios. The Spinward Marches Campaign implies very severe political consequences if Norris failed to get the warrant, if Norris' redeployments had been erroneous, if the counterattack at Efate had failed and if the trap at Rhylanor had failed.
CLEARLY, MM wanted an Imperial hero to emerge from the 5FW, a Basileus to Strephon's Justinian. That was fully demonstrated in the follow-on publications in MegaTraveller.
So I remain unconvinced that there was all that much 'deus ex machina' in the 5FW. There is certainly a lot less than Arbellatra's career, and even that is nothing compared to Avery's career.
One last thing to remember:
The GDW board games are not the RPG. Their plot lines are different. The wargame 'Imperium' is not the canon description of the Interstellar Wars, the Fifth Frontier War wargame is not the canon description of the OTU historical incident. MM has made this clear in numerous statements. They provide a combat sim if players want to game out these events, but the randomness of die rolls figure largely in the wargame end results. Those die rolls may swing one way in your playthrough but that has no bearing on the OTU.