Black water is definitely not good to hear, and Balloon Molly's have it hard enough as it is-being bred w/ a deformity-without having really hard conditions to live with. Glad that you rectified it. When you state that you 'scrubbed' the tank down, would you care to elaborate it a bit more? How did you clean it, you didn't use chemicals did you?
10g is somewhat sufficient for Molly fish, but Mollies have a larger bioload than most beginner fish (barring goldfish that is) so you will want ot keep a careful eye on your parameters. What are they? Ph, Ammonia, Nitrite, Nitrate? Fish-in Cycles are tough on fish, but with plenty of water changes you can keep fish healthy and successfully cycle the tank-I have the same guppy's and molly's that I started with over a year ago when I cycled my newest tank, so you can definitely do it.
Euthanasia is never a fun practice, but is definitely sometimes necessary if it seems that your fish is not improving but instead suffering. I have a girl harlequin molly who is about at the edge of her life, and even dying from old age is sad to see.
If you have a quarantine tank, try to separate her if she is the only one that is showing the signs and give her a good old fashioned salt bath. Speaking of salt, Molly's do best with about a tablespoon of aquarium salt per 10g of water (depending on the brand of aquarium salt), have you attempted this?
Good luck