The qconfig tool seems to serve the purpose, albeit depends on what interface you'd prefer. It takes an input file with the
CONFIG_ directives that you'd want changed, and changes them. I didn't try it yet.
I didn't try it yet, but it doesn't look like it has an interface via command line arguments, along the lines of what you described.
sed -i 's:CONFIG_X=y:# CONFIG_X is not set:g' .config
It's strange that non-interactive configuration seems to not get attention at all. It's certainly not applicable in general, but when you need to just flip a few switches (with few or no dependencies), e.g., a make target, then it would be very useful, more user-friendly than directly using
sed, and better than maintaining