It shouldn't be able to erase your filesystem unless you are running as root or doing something equally stupid. That's pretty much common sense stuff for anyone that isn't a beginner.
Yeah the "common sense stuff for anyone that isn't a beginner" argument is repeated ad nauseam, and even the largest companies make this mistake in their largest products. Take Valve - they should know how to write good code, right? And yet, last week an article was on top of HN, outlining how they put:
"rm -rf '$STEAMROOT'/*" in their code, used to remove the library. But hey, no one checked if $STEAMROOT is not empty, so when it was for one user, Steam deleted all of his personal files, whole /home and /media directories next time it started.
I'm not saying that command line tools shouldn't be used,but sometimes they are just too powerful for some users,and stupid mistakes like this happen.
You're right to an extent, but this isn't relevant to the Java vs Bash discussion. The largest companies make this kind of mistake in whatever language they happen to use.
People delete data and screw things up in MapReduce jobs for Hadoop. A lot.