By the rules as written, gentle repose only works "the remains of a dead creature." Since zombies are no longer dead, but undead, the spell wouldn't work.
However, there are plenty of ways to embalm bodies that significantly reduce the rate of decay, so there's no reason you can't just do it that way. If you're the GM, handwave it. A good embalming and liberal use of perfume should do the trick.
But yeah, if you're the GM, make a spell that *will* work on Undead, and call it a day.
One of the perks of being a GM in a homebrew game (i.e. not PFS) is that the world is clay at your fingertips. You can do almost anything to serve the story, as long as it isn't blatantly penalizing the players...