Ioncube installation takes 3minutes (most of the time it is already installed though).
Not to mention that many "de-zender" applications are available everywhere allowing you to decode zend encoded files (and they do work pretty well).
One of the cool ioncube feature is the "ASCII encoding" so your customers don't even have to configure their ftp client to upload in binary format (and believe me that drastically reduce the number of technical support tickets about installation issues!)
There is also another alternative called "Nu-coder", but this is a pretty new encoder and there is a very high change that you will have to install it manually for all your customers
http://www.nusphere.com/products/nucoder.htm 