The Rebellion movie seems to hint that
Homura's wings in this scene were indeed witch wings, or rather, the beginning of Homura's transformation into a witch.
The biggest clue is the landscape. The last time we see Homura in the series she is about to confront a bunch of wraiths in a desert landscape. The Rebellion movie reveals
that the Incubators tried to trap Homura and interrupt her witch transformation in order to draw out Madoka. When the Incubators' barrier is broken, Homura is still in the desert.
If you assume the two deserted landscapes are one and the same,
you would conclude that Homura was about to turn into a witch at the end of the series. Presumably, that's where her transformation began before it was interrupted, setting the events of the Rebellion movie in motion.