It's worth noting that news of Apophis' defeat wasn't spread immediately around the galaxy. Also, due to their belief the Goa'uld were gods, many Jaffa refused to believe that he died when they did hear about it.

It's a common misconception that after Apophis was killed, his Jaffa joined the Free Jaffa. The reality is that much of the Jaffa continued with what they were doing. Normally, they would take orders from lesser Goa'uld officers that pretended to still serve Apophis. Many ships and Jaffa would go serve other system lords after no word from their god, who they assumed had abandoned them. There was even evidence of camps where humans loyal to Apophis were being trained to infiltrate the Tauri homeworl well after Apophis was killed.

Overtime those lesser Goa'uld would use the Jaffa under their control to consolidate their power and proclaim themselves the Jaffa's new god. Such actions didn't go unpunished by the system lords, who would force those Goa'uld to swear an oath under them, or they would simply kill them and absorb the forces for themselves. This is how all the other system lords became more powerful when Apophis died.

It wasn't until Anubis fell, and later Ba'al when the Jaffa started aligning themselves with the Free Jaffa.