You can keep Linux from recording a command history by prepending one or more spaces in front of the command.
./novacoind walletpassphrase iamapassword 100000
Would be recorded in the bash history.
./novacoind walletpassphrase iamapassword 100000
Would not be recorded in the bash history.
Only if you have set HISTCONTROL with "ignorespace" which is not the default.
Edit: this is assuming you use bash and not another shell (I don't know others well enough).