I neglected to do this quest at first and only came back to it several levels later, i reached the section where you are presented with the choice to either let the werewolf kill Margrit or continue to fight and kill it. I chose the latter and continued the fight and won until the point i depleted its health bar, at this point the werewolf glitched into an idle animation and won't move or react to combat, but the quest tracker still prompts me to kill the werewolf and its location is still present on my map.

I've reloaded multiple previous saves, left the area, meditated and returned to be greeted with the same effect, even after battling the werewolf over again. It just stands in one spot and doesn't move. Any way to rectify the glitch? Or do i just have to reload a save and let it kill the woman?

Remove any mods and/or manually added scripts. If you're playing through Galaxy, verify/repair your installation.