The plan (ostensibly) was twofold: distract the leadership of the Blade Ship long enough for it to be taken down, and save Tom in the process. After all, Jake did not anticipate losing the firepower of the Pool Ship due to Erek's meddling. Had they had weapons, the Blade Ship would have been a sitting duck while a grizzly went nuts in the command center, cutting off communications and the chain of command. This would have hopefully been just long enough for the captured Pool Ship to disable or disarm the Blade Ship, to be captured later at will.
With the loss of his trump card, though, the secondary goal became all that was attainable: free Tom, which at this point was only possible by killing him. If that ship got away, then Tom would be forever doomed to wander as a slave, one of the last Human-Controllers in existence, and quite possibly out of reach forever. Jake could not permit this to happen to his brother, who he had been fighting for since the beginning of the war, but at the same time he could not from a strategic standpoint risk the rest of his fighting force for, ultimately, one person.
His conscience would only permit him to spare one person, so he sent the one expendable fighter available that could handle the bloodshed and had enough of a personal stake (however slim) to voluntarily risk dying for it. Capturing the Blade Ship would have been the preferred outcome, and was likely the cover story that he told others (and himself) to justify his actions, but at its core it was Jake's last-ditch effort to save his brother from slavery.