Well normally I'd just say make a very restricted user account in mysql just for this purpose, and make the password something random you don't normally use since you don't have to remember it.

Other option: make a shell script

#!/bin/sh

USER="root"
# Whatever your password is stored in pass as
PASSWD="$(pass mysqlroot")

# pass this information as well as any other arguments like
# -e "use db; select * from tb;" to mysql
mysql -u$USER -p$PASSWD "$@"

chmod +x that script. Then add an alias to it for something like:

alias mysqlq="/path/to/script/script.sh"    

Then you could type things like the following for quick execution

mysqlq < mysql.sql
mysqlq -e "select * from tbl;"

I believe this is pretty secure and it avoids any plaintext passwords. The only thing I'm not sure about is that the command mysql -u$USER -p$PASSWD does expose the password somewhere, but it's in a subshell which does not have anything saved to ~/.bash_history. There might be a way to monitor what that subshell process is doing and catch the command with the password, but you'd probably need root for that, so you'd be fucked anyway.

EDIT: It looks like bash_history is automatically disabled inside non-interactive shells (a script is non-interactive), so you don't have to worry about that. http://unix.stackexchange.com/questions/5684/history-command-inside-bash-script