Yep, there are a few things you can do:
1. Embed your video in a plain HTML page and then use the URL of that page as your Pay Per view content. Similar to what I have on the following page as an example:
http://www.tipsandtricks-hq.com/ecommerce/wp-content/uploads/pay-per-view.html
If you do a view source on that you can’t find the URL of that page because when I made that page I was careful about it. If you use WordPress posts or pages then remember WordPress will include all the common headers which will have the URL of the page. I have embedded YouTube videos there so it has links to YouTube but in your case I am sure you are not going to upload your secret videos on YouTube. So just use relative URL (e.g. videos/video1.flv) to embed the video on the page and no one will be able to know the actual URL of the video file either.
2. Embed the video in a PDF file then use the URL of the PDF file as your Pay Per View content. Browsers can render PDF files but if you view the source it will be gibberish.
3. Use HTML source encoder to encrypt your HTML files so when someone tries to read the source it’s unreadable by human eye.
Bottom line is that the Pay Per View content option of eStore has it’s usage but ultimately if you have super secret and valuable content then using a Membership plugin (e.g. WP eMember – http://www.tipsandtricks-hq.com/?p=1706) is the way to go.