John Komnenos’ story is found in 15th and 16th-century Greek and Italian chronicles, but those are ultimately based on the 13th-century chronicle of Niketas Choniates. The story can be a bit confusing since John shares his name with his uncle, the emperor John II Komnenos. The younger John was the son of Isaac, Emperor John’s brother (and therefore, as you mentioned, the grandson of Alexios I Komnenos).

The younger John was, according to Niketas,

“A warrior nightly and formidable in raising the cry of war, of noble statue, and most fair to look upon.” (Choniates, pg. 19)

Isaac and his son John rebelled against the emperor. It’s not really clear why, but apparently Isaac was jealous and thought he deserved to be emperor. No one else agreed, so Isaac and John were exiled from Byzantine territory in 1131, and ended up wandering around various other courts (the Seljuks, Danishmendids, Armenians, and the Latin states in Syria). At one point John may have been engaged or married to an Armenian princess. They returned in 1138 when Isaac reconciled with the emperor.

The next year, John participated in the emperor’s campaign against the Danishmendids. During a battle at Niksar, the emperor asked the younger John to give his horse to a Latin mercenary who had lost his own. According to Niketas, John was so offended that he defected to the Danishmendid side.

“A short time later, he renounced the Christian rites and married the daughter of the Turkish ruler of Ikonion [i.e. the Seljuk sultan]” (Choniates, pg. 21)

Apparently this was not exceptionally shocking. The emperor was “taken by surprise by these events”, but that’s the only reaction Niketas records.

Some time later in 1145, Emperor Manuel (Emperor John’s son and therefore John the younger’s cousin), raided Seljuk territory up to Ikonion. There he encountered John’s wife, the daughter of Sultan Masud, but Niketas doesn’t note anything remarkable about their meeting.

The 12th-century poet Theodoros Prodromos’ wrote some verses that are probably about John:

“O wild olive branch of the cultivated olive root, and unfortunate scion of a most fortunate stock, the only thorn bush in this orchard’s many trees, and only senseless member of a sensible kin” (quoted in Magdalino, pg. 423)

This is really all we know about John from contemporary (or nearly contemporary) sources. But if the details are true, the problem would be that John was now an apostate, someone who had given up Christianity for another religion. That probably would be somewhat shocking for medieval Christians! Christians who lived in frontier areas, or who lived in or around large populations of Muslims or Jews, were often paranoid about apostates. I don’t think people actually apostatized very often, but when it did happen, it just confirmed their fears.

For Muslims there was no way back, apostasy was punishable by death if they returned. In Christian church law (canon law), apostates could change their mind and come back. They would be punished, but eventually, they were supposed to be welcomed back into the community - but there would always be the problem that their friends and families might not trust them again. What if the former apostate still secretly believes in Islam/Judaism? This was also a problem for new converts.

The Byzantine Empire my have been a bit more tolerant of apostasy and the fluidity of religious beliefs. Pretty much the entire empire was a frontier - there were Muslims in the east and pagans to the north, and all around them there were fellow Christians, who believed in slightly different doctrines (whether Latins in the west or Armenians, Syrians, Copts, etc., in the east). Greek Christians were very likely to be influenced by different kinds of Christianity, or the Islam practiced by their neighbours, or the Jews who lived in Byzantine cities. It seems that the Greeks didn’t think apostasy was as serious as Muslims or Latin Christians did:

“According to Byzantine canon law of the twelfth through the fifteenth centuries, apostates and repentant apostates must have been numerous, since the church under pressure significantly reduced the punishment for such lost souls, facilitating their return to the Christian community.” (Shukurov, pg. 369)

Still, if you were going to apostatize, the best option would be to never return home, which is apparently what John did.

Later legend, derived from Niketas’ chronicle but expanded with probably imaginary details, says he took the name “Tzelepes” (i.e. Çelebi, “sir” in Turkish), and had a son, who may have been named Suleyman. Suleyman (if that was his name) was active in Anatolia after the Fourth Crusade temporarily destroyed the Byzantine Empire. Supposedly he also introduced the Turks to Byzantine law. This Suleiman was supposed to be the father of Ertegrul, the father of Osman, the founder of the Ottoman dynasty.

This legend may have originated in the 14th century during the reign of the Ottoman sultan Bayezid I, or maybe even as late as the reign of Mehmed the Conqueror in the 15th century. It may have originally been a Greek legend, a way to sort of de-legitimize the Ottoman threat - of course they’re so strong, they were really Greek all along! But the Ottomans emphasized the legend as well, as a way to legitimize their claim to the Roman Empire and to justify their conquests.

Incidentally, Isaac Komnenos’ branch of the family did ascend to the throne eventually. His younger son, John’s brother Andronikos, also spent time in exile in various Muslim and Christian lands, before becoming emperor in 1183. But his rule was brief and he was overthrown and executed in 1185.

Sources:

O City of Byzantium: Annals of Niketas Choniataes, trans. Harry J Magoulias (Wayne State University Press, 1984)

Paul Magdalino, The Empire of Manuel I Komnenos (Cambridge University Press, 1993)

Konstantinos Moustakas, "The myth of the Byzantine origins of the Osmanlis: an essay in interpretation", in Byzantine and Modern Greek Studies 39.1 (2015), pp. 85–97.

Rustam Shukurov, The Byzantine Turks, 1204-1461 (Brill, 2016)