There are a lot of third party tools that will allow you to encrypt the HTML file. Actually there is nothing in the HTML file generated by Labview, because the run time Engine does the Magic.
Anyway I use HTMLock which can be purchased for $25. There are some freeware tools too. I like HTMLock because you can pass your HTML file once and that encrypts it. On the second Pass I implement Password protection. So now if you go to the web Page, It asks for Password. If you try to see the source for this page, it is encrypted. If you know the password, you can view the VI and again the source is encrypted.
The site is
http://www.atrise.com/htmlock/
Good Luck!
Mache