I'd say Kill la Kill is more of a regular parody of shounen. Then again, my only frame of reference for mahou shoujo is Madoka, so I don't have the strongest grasp on what magical girl shows are all about.
Hmm. I'm not super Genre-Literate when it comes to Manga/Anime (thanks BTW Reelya; I'm educating myself on Josei as I write!), and though it's kinda pointless to try to label it, I was still trying to figure out what category to lump KlK into.
It seems like it walks an unusual middle line, combining bits from Magical Girl and Shonen/Seinen "Big Damn Hero" sort of stories. On one hand, the MC is a girl struggling to find a community, friends, and a sense of belonging, despite being abnormal and an outsider; on the other, she's a scrappy lone wolf drifter with a big sword and a murder to avenge, and she's ready to take on anyone that stands in her way. The Mahou Shoujo Transformation Sequence trope applies to male and female characters alike, with outfits for both that are revealing or humorously Gaze-y (as illustrated by Max™). The problems the story presented were generally solved in huge over-the-top fights, but they weren't overcome by strength alone; the aid of friends, community, and family were vital to most (if not all) victories. Along with the DBZ-style "being close to death only makes them stronger" trope, self-love and self-acceptance, the love and emotional support of others, etc. were literal sources of power.
So yeah... it's hard to say, but it seems like a bit of both. That's why I just shorthanded that to "Mahou Shoujo Deconstruction".