Ok, here's where the entire series falls apart for me.
I understand the need to write stories like soap operas in order to gin up more book sales, however I'm absolutely stunned and disgusted by the lack of logic evidenced by any of the writers beside Abnett wrt this series.
Mars, the home of all the ordinance that the Emperor will need to fight Horus, is abandoned? In fact at one point in the story, the author notes that the Imperial battle fleet retreats from orbit as the pro imperial and anti imperial Mechanicum forces battle it out above Mars....
I mean, wtf?
I kept reading this series thinking that there was some cosmic reason that would be revealed, that all of the moronic inconsistencies would be finally drawn together into some kind of coherent plot line. I would have accepted the Emperor as a Chaos agent at this point, but more and more this series by comittee approach to writing this history is not only maddeningly illogical, but it's becoming increasingly unreadable.
Ok well here is how I rationalise it
By the time of the civil war on Mars (the result being a victory for Horus) - The Emperor is strapped to the Golden Throne, basically unable to do anything, but keep the Imperial Webway conduit sealed, so he isn't in direct command. Malcador/Dorn is acting as regent.
There is not a particually heavy concentration of Imperial Forces in the Sol System at this time, although Dorn has recalled several Legions to make ready the defense of Terra (but they havn't arrived yet):
The Space Wolves were on Prospero.
The Ultramarines were at Calth.
The Raven Guard, Iron Hands and Salamanders had been decimated.
The Imperial Fists had garrisoned Terra.
The White Scars were acting in the Chondax System (near Prospero).
The Dark Angels were acting in the Shield Worlds.
The Blood Angels were getting massacred in the Signus Cluster (Signus Prime).
At the time of the fall of Mars, Dorn couldn't really launch a full scale invasion of Mars to reclaim it, he had only part of his legion (the rest having been ambushed by the Iron Warriors en route to Isstvan V) - and invading Mars would probably have crippled his legion. They were needed as close to full strength as possible for upcoming Siege of the Imperial Palace.
Mars was totally and utterly lost, and the Dark Mechanicum was in complete control. With everything else going on and resources at this point stretched thin, Dorn (sensibly in my opinion) orders a few companies of Imperial Fists to secure certain factories/forges on the surface of Mars and make off with vital equipment/supplies. Tactically this was the right thing to do and it would be a waste of Astartes and resources to attempt to help any remaining loyalist members of the Mechanicum on Mars.