It doesn't apply only on the beginning of the fight since it's not a buff that gets applied on your ninjas at the start of the battle. You'd have to test if Sakura's slugs are Konoha tagged. If yes then they are indeed protected by Chiriku's passive.

EDIT: To test this you could either compare the damage done to your slugs with and without Chiriku or get Yagura to copy someone elses Iruka to see if Iruka applies a shield to the slugs.