I think the problem is actually simpler than some of that. Of course, this may just be previous experience with AS talking. We should probably just simply write those scripts as a first test case to get a better top-down view instead of an inside-out one, in any case.
There's an interesting detail you've brought up here though: Conditional scripts. A script shouldn't even be created if it's dead or doesn't meet the necessary requirements. Of course, these would have to be set up in the editor first unless we do one of the following:
1) Expand script metadata so that users can make script objects themselves conditional,
2) Expose conditional variables to scripts.
...Maybe something else?
At any rate you guys can have fun with it. There's probably lots of cool stuff that can be done as it progresses, I'm sure.