Uh... keeping the thread back on (off-)topic...
The Colossus was finally destroyed because it was fast becoming a nuisance, and a Ravana was incapable of handling the situation. That's why. To reiterate, with the Master Plan so close to completion, not much else mattered. If the Colossus had been with the Bastion, the Ravana would be going about its business elsewhere. Fighters and bombers only were being sent to attack the Bastion. If the Colossus had been with it, the Shivans wouldn't have cared. IIRC, the Bastion was sent to close off the Epsilon Pegasi node. Essentially, it was retreating. According to the nodemap (which neglects to label Epsilon Pegasi (and shows Procyon A as completely isolated from allied systems at the time of the rebellion - WTF?)) the Bastion would have been heading back to allied space, through the systems previously controlled by the NTF. The Shivans would have considered this another fleeing ship and assigned only the usual to attack it; loads of fighters and bombers.