How to use Ctrl+C to stop whole script not just current command

Ctrl+C sends the interrupt signal, SIGINT. You need to tell bash to exit when it receives this signal, via the trap built-in:

trap "exit" INT
for ((i=0; i < $srccount; i++)); do
    echo -e "\"${src[$i]}\" will be synchronized to \"${dest[$i]}\""
    echo -e $'Press any key to continue or Ctrl+C to exit...\n' 
    read -rs -n1
    rsync ${opt1} ${opt2} ${opt3} ${src[$i]} ${dest[$i]}
done

You can do more than just exiting upon receiving a signal. Commonly, signal handlers remove temporary files. Refer to the bash documentation for more details.