The support for the Monkeys being feral transformations of the Kokiri stems from a partnership between their roles in both MM and TP. In MM, there were equivalent races of every race from Hyrule, even the Sheikah. Both the Sheikah and the Ikana were absent from Hyrule and Termina and both lived in villages with a well, a music-box related building (Windmill Hut and Music Box House), and a graveyard. In the forest region of Hyrule, the Kokiri lived in their own village, the Kokiri Forest, and the Deku Scrubs lived in the wild Lost Woods. In Termina (remember, designed oppositely of Hyrule), the Deku Scrubs lived in their village, the Deku Palace, and the Kokiri? Well the Kokiri had no leadership, no Deku Tree, so they took the wild forms of monkeys and lived in the Woods of Mystery (equivalent of Lost Woods).
A century or so later based again in Hyrule, the monkeys reappear in very similar apperances. What again is missing though? A Deku Tree to lead the Kokiri. This is why I believe the monkeys are the Kokiri.