Are there historical secret services like Section 31 that began as organizations of loyal undercover citizens?
Short answerGovernments usually suppress or control such groups because loyalty to a self-defined national ideal can diverge from lawful authority; the Pinkertons are offered as the nearest partial example, but they served clients and paymasters.
NotesA government is expected to distrust an independent body of citizens claiming authority to conduct secret operations on its behalf. The Black Dragon Society illustrates the risk of loyalty to an ideological vision that diverges from official policy. Pinkertons provide a partial analogy through paid private security work. Paid guards such as the Varangians offer a different model of loyalty to a ruler. Absorbing an independent service would still leave the question of whether its members accepted government direction.