Hi!
As far as I know, there isn't such a direct 'save' command on the S switches (without having to answer 'yes' as a confirmation).
There is a provisional solution, naturally, just paste 'save' and 'yes' in separate lines followed by the empty line (or CR-LF at least):
save
y
It's not a perfect, but rather a primitive solution :), but it works in many cases (sadly, not with the 'execute batch-file' command).
You can also use 'set save-configuration" to atomatically and periodically save the configuration file after the changes, but I don't think that's what you're looking for.
Regards,
Piotr