Not the end of the world
Running ANY programming language inside the web-browser is a bad idea. The more capable the language, the worse idea it is. If you can change the web-site applets can trivially be changed into jnlp downloads solving the problem. If you need to access an applet based interface that has not been converted then just open another browser when you need to (you could even write a stand alone program specifically for running java applets from web pages). Lets face it java applets never integrated well with the surrounding web-page so losing the ability to start them seamlessly is no big loss and easily worked around.
Biting the hand that feeds IT
