That's indeed the core of the problem. If your server is properly set up, you probably have one unix user per app, with other home directories not traversable and you can simply add a temporary ssh key. But then again, if customer have difficulties to install your software being just a php / mysql app, chances are great his server is not properly set up.

I think that the proper solution to any paid, self hosted application would be ... to provide hosting for less tech savvy users. Granted, your main selling point is to be self hosted, but you should not alienate people who are interested just by the product itself. And having a less costy per month plan is a great mean to let users try your app before deciding they should takes time or money to educate or hire a sysadmin.