In BeOS 5, Be makes it much more difficult to accidentally delete important system files from the Tracker. Try deleting anything under the /boot/beos hierarchy and you’ll get a warning dialog requiring you to hold down the Shift key while pressing OK. However, this „idiot-proofing“ doesn’t extend to the BeOS shell.
If you want a similar level of protection when using the Terminal, try this:

cd /bin
chmod 555 *

Repeat for any directory in which you want overwrite protection. To delete things from this directory, you’ll now need to chmod them back to a user-accessible permission level.