I've never used kermit, so this is a guess. I'll bet kermit is starting a console that you then enter the commands "set ..." and "connect" into.
But when you run it as a bash script, the kermit command starts and bash will wait for it to finish before running the next line of the script. (Bash doesn't know to send the two lines to kermit. Its going to try to run them as if they were bash commands).
Try something like:
echo <<EOF | kermit -l /dev/ttyUSB0
set carrier-watch off
That'll run kermit, and then pipe everything until EOF to it. <<EOF is called a heredoc and the pipe is called a pipe. (Its the thing by the backslash).