I'm assuming that both of these works are canon, but there are a few plot conflicts that I'm having trouble resolving. Is there anything that explains these differences in plot? Does the game completely retcon the book? Do the book and game conflict or is there some way to convincingly explain the differences to ourselves?
In the book:
The UNSC forces prepare for their mission with Cortana and Master Chief participating in various drills while Reach is seemingly not under attack. The plan is for them to go on a mission to capture a Covenant prophet. Before the mission can begin, the Covenant pull a complete surprise attack. There's some action involving attempting to disable the orbital defensive MAC cannons. Ultimately the planet is very quickly destroyed. The Pillar of Autumn barely escapes.
But in the game:
There's drawn out military campaigns and land battles over what seem to be days and weeks. The spartan "Red Team" (Master Chief's team) is alluded to be taking part in civilian evacuations. The Pillar of Autumn is sitting in dock waiting for you at the end of the game. Presumably they leave right away for Halo with a covenant fleet in pursuit.
This difference is particularly glaring, from the Halopedia article.
Captain Keyes orders the Pillar of Autumn back towards Reach, but the Master Chief convinces him to allow the Spartans to continue their mission by finding a damaged Covenant ship to capture and take to Covenant space.
It seemed at the end of the game that Reach was written off and done for. They were escaping a covenant attack to initiate their important mission. Given that why turn around or be at all surprised that another Covenant fleet shows up to attack Reach?