Ah, I see what you’re saying. Unfortunately I only turned this code: https://code.google.com/p/html5slides/ into a WordPress plugin, so I’m not sure if there is a way to do what you’re asking.
One thing you could try is adding target="_blank" to the link: <a href="http://chris.crowntasticmedia.com/hot-beverage-bundle-guide-v2/#3" target="_blank"><span style="color: #993300; background-color: #99ccff;"><strong>Move to Hot Beverage Pitch</strong></span></a>
The downside to this is it will open the link in a new tab/window.
The main intention for this plugin is to create presentations for talks and such, so that type of functionality would be unneeded for that context.