Hi,
Java fern are very tough plants and can take a 4 minute dunk in a 1-19 solution of chlorine bleach and water. Mix 1 part chlorine bleach in 19 parts water. So 1 ounce chlorine to 19 parts water. If you need more mixture just use more bleach and water, i.e. 2 ounces bleach to 38 ounces water

If you use this method on more tender plants, such as stem plants, only leave them in for two minutes.
Then place the plant in this solution and time for four minutes. Rinse very well several times in unchlorinated water. It is a good idea to use a chlorine remover in the water just to be on the safe side.
After the plant is thoroughly rinsed and there is no chlorine smell left on it, you can then put it in the tank.
This will take care of algae, too. I have done this for many years, and I cannot attribute any disease to my plants. I have two heavily planted tanks.
The little plants growing on the leaves is just the java fern's way of creating new little java ferns

Left on their own, they will eventually break free and float around the tank looking for a place to lodge. You can remove these carefully. If you damage the big leaves, the damage will pretty much remain, however, you could carefully trim the leaf so it doesn't look so bad. Also, don't be alarmed if you see little black dots on the leaves. These are normal.
Valerie