Ganju's had a lot on his plate ever since Aizen made his ascension into Hueco Mundo that fateful day. He just hasn't been able to do anything about it. The Shiba clan was outcast, though once it became clear that they'd all been betrayed, Kuukaku's reclusiveness came to an end. Maybe she wasn't the most diplomatic person around, but she made damn sure her voice was heard regarding the matter, and offered to help wherever she was needed.
Naturally, that meant Ganju was expected to help as well.
There were months of bickering, with little for Ganju to really assist with other than running messages back and forth on Bonnie-chan's back. The outcast Shibas lacked the luxury of Hell Butterflies. Either that, or Kuukaku was just being a vindictive big sister. That happens too.
While the destruction of Karakura didn't really impact Ganju on a personal level, given that everyone he knew from that town had escaped unharmed, he still wept manly tears for its loss. Ten thousand souls abruptly ended in the blink of an eye, never again to be reborn, is a terrible tragedy. He grew tired of feeling useless, and against Kuukaku's better judgment (as well as his own), he decided that it was time to put aside his old prejudices once and for all and enlist as a shinigami. He still has a tough time relaxing around a majority of the shinigami, particularly the rowdier ones in the 11th division (if they want a fight, BRING IT!), but he understands how important it is for everyone to pull together and stand firm, no matter how long it might take to someday overthrow 'the benevolent dictator'.