So, this question is quite big but let's clarify a few things. The time period commonly known as the "Dark Ages" has been examined and re-examined lots in decades among academics, and I personally prefer 'early middle ages' until the 11th century. Someone else will hopefully shed some light on the Maniots as I have not studied them. My own studies as an undergrad are in (late) antiquity, so that's what I will talk about. I will attempt to explain how paganism still existed in the 4th century, and what measures were taken to limit its influence in an increasingly Christianizing empire.

To begin, paganism was far from extinct in the 4th century! The emperor Constantine legalized Christianity, but did not outlaw paganism, nor does it seem like he completely abandoned pagan elements in his own administration. Many churches, but also pagan temples, were built in his new capital of Constantinople. Throughout the 4th century, as only one out of 21 emperors was pagan and the creation of some kind of unifying religious ideology can already be seen, laws were enacted banning certain pagan practices such as animal sacrifices and divination. But paganism itself was never banned and influential pagan families still existed among the senatorial classes. The various cults that we lump under 'paganism' weren't yet gone and the scale of temple destruction across the empire was far from apocalyptic. These seem to have depended on the size of the Christian and/or pagan communities in the area, what kind of man was appointed governor (there are examples of both pagan and Christian governors during Theodosius' reign at the end of the century, he also made Christianity the state religion) and their interpretations of the law. It was one thing for an emperor to wish to impose religious unity; it was another for them to have been able to put that into practice.

By the 5th century, Christianity has thoroughly become the state religion legally and socially with bishops now ranking alongside (and often coming from) the powerful senatorial families of old. The contention between pagans and Christians has now been largely replaced (though not yet gone, as Orosius would call the 410 sack of Rome a punishment from God due to, along with general decadence, pagan elements within the city) by competing Christian creeds such as Arianism and the 'Catholic' Nicean Christianity. With the fall of the Western empire in the late 400s most kingdoms in post-Roman were Christian of some kind or another with the Franks converting in the early 500s to Catholicism, the Visigoths and Ostrogoths in Spain and Italy were Arian.

In the eastern empire we see the last official vestiges of paganism disappear under the reign of Justinian. Notably the 529 forced closure of the School of Athens, a bastion of Neo-Platonic philosophical thought. The Justinianic law code prohibited pagans to hold state office and featured further edicts against pagans, but mostly they were lumped in with Jews and those that were deemed heretics by the state church.

The religious dominance of Christianity in post-Roman (and still-Roman) Europe was at this point a fact and though far from unified or all-powerful (it would waxe and wane in terms of its political influence over the centuries) it remained the only option available for rulers throughout the post-Roman world. You still had pagans in Europe for centuries, especially beyond the old Roman borders but the worship of the Greek gods? There is no real evidence for any king or royalty to have worshipped these pagan deities. These traditions were not forgotten, as continuing literary cultures in the Roman and Islamic worlds kept some of the philosophies and stories of the past alive, but they were no longer the religion of anyone of note.

I have not done any research into the religion of the Maniots; to what extent were they indeed pagan or to what extent this was a definition given to them by Christians. Unless they had kings the answer to your question is a 'no'. Many kings in Europe did not come from a Hellenistic religious tradition anyways, either being Arian Christians (Visigoths, Ostrogoths, Vandals) when they began ruling their new kingdoms, or pagans (Franks) in their own traditions. In the east, the surviving Roman empire was endowed with such Christian importance that it was the 'Christian Empire' and Hellenistic paganism, if it survived, only existed in small communities of no real importance. You would never see it practiced in an imperial or royal context again.

Here are some books and collections of articles I looked at when writing my answer:

A Companion to Religion in Late Antiquity (published by Wiley Blackwell)

Pagans and Christians in Late Antique Rome: Conflict, Competition, and Coexistence in the Fourth Century (Cambridge University Press)

From Rome to Byzantium AD 363 to 565: The Transformation of Ancient Rome (Edinburg University Press).