The plan was indeed to blow the Crown of Thorns up:
“THEY’D COME UP with this really great plan to keep their mysterious pursuers from blowing up the Crown: they were going to blow it up themselves first.”
However instead of using an escape pod, the bicameral’s separated the drive section from the habitable parts of the ship.
Looking at the plans of the ship from the authors website, the sections marked ‘habitable areas’ were powered down and detached, while the drive section kept firing and blew up.
“Brüks squinted, tried to squeeze signal from noise through the cotton growing in his head: the Crown’s drive section was already kilometers to port and kilometers ahead, its lead increasing with each second per second. Tactical had laid a vast attenuate cone of light across the space before it, spreading from the abandoned drive like a searchlight. Ramscoop, Brüks realized after a second. A magnetic field to gather up ionized particles, a brake against the solar wind. A proxy for mass gone suddenly missing: no telltale change in acceleration, no suspicious easing back on the throttle. One measure among many, shoehorned in between the masking of heatprints and whatever stealthed this ship to radar. Moore had told him as much as he could understand, Brüks supposed. There would be more.”
Once the powered down habitable section had drifted far enough away from the pursuers search, the bircarmal’s built a (much smaller) replacement engine in the hold.
Essentially the configuration of the ship after the gambit is just the habitable parts from the diagram.