Yes, turning off the ability to execute arbitrary code on your server through your web browser will, indeed, turn off the ability to execute arbitrary code on your server through your web browser. I think that is a misfeature: if executing arbitrary code on your server could potentially do damage to your business (hint: yes), you should be SSHing into a terminal to do it. That combo will be 500,000x more effective at securing your box than the best efforts of Wordpress, PHP, and the fifteen year-old designer who coded your lightbox plugin after Googling "How to find file name in PHP".
See also my comments last week about the (lack of) wisdom in embedding a ruby shell in a web application.