Can my employer retaliate against me for filing a final paycheck claim?

No, at least not lawfully. Retaliating against a current or former employee specifically for filing a wage claim is itself illegal under California law, entirely separate from whatever the underlying wage dispute is about.

If retaliation does happen, that's a distinct legal issue, and claims about it are generally handled by the Labor Commissioner rather than through small claims court. If you're still currently employed by this employer while considering a final-paycheck-related claim, that ongoing relationship changes the practical calculus enough that it's worth talking to someone knowledgeable before filing anything.