The Astartes and the Imperial Guard both are part of the Imperium, but both work largely independent of each other. There have been quarrels between them on numerous occasions. Same as with the Sisters of Battle. (With numerous occasions, I do not mean the Dawn of War games).
Soulstorm was lore-breaking You can't put imperial guard/space marine fighting an inquisition division (sisters of battle) and expect no serious backslash to happen