While you could just have the normal versions of the Pixelmon structures spawn there, I think that Zombie villages should have their own "zombie villageified" versions of these structures, including the Daycare (which is just the normal one right now). They would be almost identical to the normal versions (unless you feel inspired), but they would have no doors, random blocks would be replaced with cobwebs, there would be no torches or other light sources, normal glass panes are replaced with brown glass panes, and the majority of cobblestone blocks are replaced with mossy cobblestone. Basically, the same changes that occur to the normal houses in zombie villages.
I'm not a builder, but I don't think this would be too hard to incorporate, especially with world editing tools. You'd just have to look at the normal Minecraft houses and the zombie village houses side-by-side, then copy and paste the Pixelmon village structures and make the changes that match the changes zombie villages make to their houses.