htaccess - hosting multiple domains on one shared server, - .htaccess

Question

I have a site1.com as my primary site. I created two folders in the root directory "site1" & "site2". I used Htaccess to redirect site1.com's traffic to folder "site1". Site2 works too as site2.com using directory "site2".
Now, the issue is because site1 is primary, I'm able to visit site2 via site.com/site2 . What rewrite can I use to ignore site.com/site2, or show a 404 when site1.com/site2 is visited and still allow for site2.com to work?
Here is my htaccess file.
RewriteEngine on
Options -MultiViews
RewriteCond %{HTTP_HOST} ^(www.)?site1.com$
RewriteCond %{REQUEST_URI} !^/site1/
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ /site1/$1
RewriteCond %{HTTP_HOST} ^(www.)?site1.com$
RewriteRule ^(/)?$ site1/index.php [L]
RewriteCond %{HTTP_HOST} !^www\.
RewriteRule ^(.*)$ http://www.%{HTTP_HOST}/$1 [R=301,L]
RewriteCond %{REQUEST_FILENAME} !-d
RewriteCond %{REQUEST_FILENAME}\.php -f
RewriteRule ^(.*)$ $1.php
My folder hierarchy is
-root
.htaccess
-site1 folder
- index.php
-site2 folder
- index.php
Due to godaddy's primary domain setup, even though when i visit site.com it loads info from site1 folder, if i visit site1.com/site2 it will load site 2

Answer 1

I went in a different direction for a similar problem on Godaddy.
Rather than looking for just hits from site1.com and redirect them, I sent any requests hitting the site2 subfolder / subdomain to site2.com with this:
RewriteCond %{HTTP_HOST} !^site2\.com$ [NC]
RewriteRule ^(.*)$ http://site2.com/$1 [R=301,L]
Now any requests that worm their way into that site1.com/site2 subfolder get 301'd to the appropriate page on site2.
I don't consider myself an expert by a longshot and would welcome critiques from those with more experience.

Answer 2

Untested code: I believe you can do the following
RewriteCond %{HTTP_HOST} ^(www.)?site1.com$
RewriteRule ^site2/(.*)$ http://site1.com/$1 [R=301]
This will (or should) redirect the client from http://site1.com/site2/my/awesome/page.php to http://site2.com/my/awesome/page.php.