that would get you stuck in a neverending loop. linking from your website to the intro would play the intro, you would get redirected to the main site, only to get redirected to the intro again. think about embedding the swf on your main page but editing the swf to not redirect you to the home. I mean:
1. intro swf plays on main page through embedding
2. intro swf finishes
3. scroll down to see main page.
you would also need to put
stop(); on the last frame of your swf to prevent it playing again.
ps I'm only 12 so if this doesn't work don't blame me!! :D