Both of the above articles discuss the legitimacy of Maelstrom missions. Both of the articles placed Maelstrom missions as either not suitable for tournament play or required serious modifications to be viable.
With experience in a number of other long-term tactical war-games, I don't think that random objectives are so random that it necessitates removal from competitive play. One example of a game that uses random objectives to great effectiveness is Twilight Imperium 3. The game relies on these random objectives to secure victory. They are somewhat similar to the Maelstrom objectives in their scope, which is to say that one success in a particular element of the game leads to victory. Obtaining a certain amount of technology cards in TI3 (the abbreviation for the game) will gain you one victory point.
The major difference for these objectives, in TI3, is that they are public and available to both opponents. Players can score the same objective in the same game round, and they sit for the entirety of the game.
My thought is to apply this concept to the Maelstrom of War missions. Make each player fight for the same objectives. If they have a D3 option, standardize it at 2 (similar again to TI3 with Stage 2 objectives, which are harder and therefore worth more points.) These same objectives sit throughout the game, and whomever earns the most points wins. You can then establish a certain series of tiebreakers throughout the mission to handle ties.
There are some games of TI3 that create objectives that are just so difficult to achieve and often are ignored as potential objectives. This is the nature of the game though, and instead of feeling like the player has nothing to do, the player normally just tries to advance their board state. This is true in 40k as well. If you can't score Maelstrom objectives, you can certainly aim for destroying enemy units and increasing your chances of victory.
I think this version of Maelstrom of War could be very interesting. I will be posting more of my thoughts as I develop them.