Extension associations are based on syntax highlighting schemes.
To remove unwanted associations, open ST2 and choose Preferences → Browse Packages..., a folder with packages will open. Find the incorrectly detected package (in this case Lisp) and open a .tmLanguage file (Lisp.tmLanguage) in ST2. It's first lines look like this:
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE plist PUBLIC "-//Apple Computer//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
Those strings in lines 9-13 are file extensions that ST2 will associate with Lisp. You can remove some of those lines (place the cursor on unwanted line and press Ctrl+Shift+K), changes will be applied immediately when you save the file.
To add new associations, open a .tmLanguage file from a package and add new strings among those already defined.