Figured I’d give you the heads-up ASAP because eventually we’re all going to have to work out how this goes.
You are right - if you don’t pay Apple $99 and then sign your application with a Developer ID then when someone using Mountain Liar tried to run your program, they are prevented from doing so. They can turn this off in general from a control panel, deliberately open the app with a left-click menu item, or execute a command line statement to mark your application as OK.
I particularly expect a lot of my users to fire up a Terminal and type some shell commands in, because that’s one of those things users are good at. [/SARCASM]