To throw good money after bad means to try to recoup initial losses by spending more money, but in this context they can't afford to waste more money.
Consider the statement "He wasn't sure she'd find enough clients in chance creek, anyway, and they couldn't afford to waste more money on something that was already a lost cause.". Is the statement "He wasn't sure she'd find enough clients in chance creek, anyway, and they couldn't afford to throw good money after bad." false? Yes/no/unknown