I mean, ultimately, you are the arbiter of whether or not the plan succeeds. I could see a few "buts" "ifs" and "whens" along the way myself. I wonder if the following scenarios would have been easier:
1) hide the girl somewhere. Polymorph can still be useful in this instance to disguise her identity.
1b) you could even disguise someone else as the girl in this case- bonus points if you polymorph the most badass warrior you can find into a 14 year old girl- wouldn't that be a surprise for a would-be assassin?
I had a few more, but they require other spells, and you did say that, for whatever reason, the caster lacked other spells to use.
When discussing morality in D&D there are two kinds of morality to consider. Real world morality, where ends can justify the means, and the "cosmic" morality of the Outer Planes, where Good is Good and Evil is Evil and the ends never justify the means.
Performing a potentially Evil act for a Good cause is still Evil to the Gods and powerful entities of the Planes, because that's how the D&D multiverse functions. Good, Chaos, Law, and Evil are cosmic forces unto themselves that can't be argued with, reasoned with, or accept compromise. They are and that's all one can really say about it.
If armed with a scroll of Polymorph and I needed to prevent the girl from death, I could certainly justify doing something horrible to her in the short term if it led to an ultimately Good act- like turning her into a stone statue and stashing her someplace until it was safe to reveal her existence to the world.
But in the eyes of the Gods, I still did an Evil thing, and will pay the price for that down the road.