I think, if I read it correctly, then yes, that's what I would do. Any variable and script initialization - basically anything you're trying to "set up" for later, I would run from the init.sqf. For instance, in my typical init.sqf, I have a section for initializing variables, calling scripts for dynamic content, core scripts that run the entire mission, etcetera.
On of the biggest reasons for using the init.sqf is to make sure that all of your variables and such for later on exist. If they are not initialized before a script runs, the effects can be hard to trace back to the problem.
By putting all of that stuff in the init.sqf, you don't need to execute/define a lot of stuff in game because the init.sqf is automatically executed by ArmA.
Hope that helps.