Does killing fbserver process on Linux do any harm?
Short answer: No, if you use Firebird 2
In previous Firebird versions (1.x) the only way to safely shut the SuperServer down was to use fbmgr/ibmgr program like this:
/opt/firebird/bin/fbmgr -shut -user sysdba -pass ******
Since this requires SYSDBA password (even with root account) to be stored in system startup/shutdown scripts in plain text, an alternative had to be found. Standard POSIX signal handling was added in Firebird 2, and sending signals 2 (SIGINT) and 15 (SIGTERM) to Firebird server shuts it down cleanly. So, it is safe to run...
# killall fbserver
...to stop the server (killall sends SIGTERM by default). If server process is 'stuck' for some reason, it might not handle those signals, and the only way to kill it is with SIGKILL (9), which is forced kill without any cleanup. You should avoid this if possible:
# killall -9 fbserver