I finally decided to save a copy of the mission to figure out why Volition decided to disable the Colossus. So I give the Colossus her engines back so that she would run her waypoints (since they are still in the events).
I figured out why.
It wasn't so much the Sathanas, but it was the Ravana. When the Beast jumped in, it wasn't able to fire a salvo as she was behind the Colossus and out of range. But then the Colossus doesn't turn to engage the Beast, so it takes a good 5-7 minutes for the Ravana to get into a firing position. Then she's able to fire a couple salvos before she gets into the Colossus' ventral firing arcs and gets overpowered.
However, the dual between the Colossus and the Sathanas was in my opinion, much more satisfying than the default version where the Sathanas just comes in and rapes the Colossus. The Sathanas comes in and fires one salvo, but then has to turn to avoid hitting the Colossus. The Colossus fires up her engines and travels alongside the Sathanas and broadsides the juggernaught. But, the Colossus isn't at full strength and she's in the firing arc of that rear LRed. I kept my fighters back to watch the action, and after dueling for about 3-4 minutes, the Colossus finally succumbed to its fate.
Like I said, it was much more satisfying. But then I like slow paced battles so maybe my opinion is biased.