First, Zend Core had an older version of a toolkit to allow calls to IBM i CL programs and functions. We have discontinued that in favor of this newer version developed jointly by IBM and Zend but you could start start with that older versino to get stuff running and later during the transition change a few lines and move to the new toolkit. Try to keep your CL calls isolated into one file/function so it's easy to swap out if you can.
Second, I'm not 100% certain but it might even be possible given the nature of the new toolkit that it could be made tow ork on Zend Core. Maybe some of the more toolkit knowledgeable people have more thoughts.