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If I wanted to release what I thought was a useful script on a website, is there a way Adobe or myself can protect against accessing or reverse engineering the code?
You can save it as a jsxbin file, which sort of encrypted, but people have already found a way to reverse engineer that. So as JJ said, "No," but for the average user, then you could use the jsxbin file.
It not the average user that wants to steal JSXBIN code. And google will help the average user it they want too.
Decode Decrypt JSXBIN
Aside from what the others said, even in a compiled script the individual actions that trigger functions in the host program can be traced, so it's easy to figure out, no matter what.