HTML replacements "kill" body JavaScript

[GoogleCodeExporter]

What steps will reproduce the problem?
1. Open any page containing scripts in the body
2. Do any innocuous HTML substitution (e.g. "asdf" to "asdf", matching case)

What is the expected output? What do you see instead?
Page should continue to work exactly like before, but it stops to work as 
intended. For example, trying on google.com, before substitution instant search 
works, after substitution it doesn't.

Please use labels and text to provide additional information.
Possibly related to issue 17. It's also the same problem described at 
https://addons.mozilla.org/ca/firefox/addon/foxreplace/reviews/358675/

Original issue reported on code.google.com by [email protected] on 26 Jul 2012 at 11:58