If Jake had freed Tom then they would have been screwed from the start. Do you think the Yeerks wouldn't notice when one of their high ranking members suddenly vanishes? If Tom had been freed, the Yeerks would have gone right after his family, who would have been taken or been forced to flee, exposing Jake as a part of the resistance. After that they'd go after people connected to him, such as Marco, Cassie and Rachel. Even if they all escaped somehow, they'd have been on the run for the entire series.