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I think meaning that it may not endorse different films after your video has completed playing. You will possibly nevertheless have all the ads shooting up during the video though which is not ideal. like you can see here on the amazon gift card website.

Cyklop Studio is correct. Definitely the second option. 301 your pages, change all links, then crawl your site so you can find any links you missed. Imagine for a moment you moved to a new home. You go to the post office and forward your mail to the new home (i.e. a 301). Would you still keep asking everyone to send your mail to your old home (i.e. keep the old links)? No. You would update everyone you can, then as you notice forwarded mail you can contact those people or businesses you missed and alert them to your new address.

I personally wouldn't rely on the advice of just one company that 'your domain is toxic' (whatever that might mean). In order to make such a drastic move, I'd first get a second opinion on this, or run the site through some tools. Perhaps the company doing the SEO just isn't capable enough to get your higher rankings? What arguments are they presenting that might be causing the 'toxicity' for your domain?

Worthwhile having a watch of this http://www.seomoz.org/blog/preventing-linkbased-penalties-whiteboard-friday