I imagine that if Shino were to defect from the village, it would take place one day after he failed to protect his teammates. Leaving Kurenai's group and eventually leaving his clan feeling quilt and shame.
He might live on the outskirts of the village for a while at first, thinking things over before officially deciding that he wants to leave.
It would be next to impossible to track him down since his bugs cover up his scent. The Inuzuka and Aburame both would have an exceedingly difficult time. He could be completely off the grid.
If the Aburames act like a hive and can share/pass on bugs, Shibi's bugs might have a special connection with Shino's bugs that allow him to be found.
If Shino was found one day and escaped, he'd probably be prepared to replace his type of Kikaichu. Find a new bug to host so that he can't be found so easily again.
He might take odd jobs like pest control to earn some money since he isn't taking missions anymore. He would just command the invasive bugs out of the home/building and relocate them somewhere safe. He might even take on a farming job to use his bugs to help pollinate the plants and crops. He's even considered bee keeping.
I don't see him as being a malicious or dangerous entity when defecting. He would just want to be forgotten and become a grey-man.
He could be constantly traveling as he might attract bugs towards him. That and his clan ecologists would notice the bugs he relocates from pest jobs suddenly popping up in a new area of a forest.
Hinata, Kiba, Kurenai, and his clan would never forget him. His team would hear about a new occurrence of bugs popping up and go to investigate the spot hoping it would lead back to Shino. His father wishes he knew how Shino felt before he left the village so he could try to have convince him to stay.
