My first scope was an ETX-90EC. Meade makes a micro-focuser that fits tightly along the back of the barrel so that it can still achieve zenith. This focuser was controlled by the autostar and has the part #1244. It appears that JMI also makes one though I have no experience with it.
The problem you might have though is when trying to find focus, the image will shift, so the auto-focus routine may not work.