I appear to be having trouble removing Reference Aliases or their attached scripts from Actors. The only function I found to be remotely resembling what I want is clear(). Is there something else I need to do?

I have had a lot of trouble with alias' as well.
I haven't quite understood it completely yet, but I know this much: There's a difference between "Alias" and "Reference Alias" - this caused me a lot of trouble.

Here's what I would suggest you try: "TryToReset()"

http://www.creationkit.com/TryToReset_-_ReferenceAlias

According to the wiki:
"This is a convenient way to reset a reference in an alias without calling GetReference() on it."
If I understood that correctly you don't have to mess with the Alias/Reference Alias - issue.

You could also try: "TryToClear()"

http://www.creationkit.com/TryToClear_-_ReferenceAlias