This website uses Java where? I have Java disabled in my browser and can navigate and use this site just fine.
The website does use Javascript, which is entirely different and unrelatd to Java.
Similar to the OP's concerns, I've seen it suggested lately that it's time to put Java to bed - that 90% of computer users never use it, that Java's risks outweigh the gains. Eg. http://www.pcworld.com/article/261843/time_to_give_java_the_boot.html I don't know how valid the report is, but it seems to be a cause for concern.
How would that affect Arduino,if Java was no longer available (or at least no longer pre-installed) on new computers?