OK, well there are a few approaches you might take. But perhaps you need to define "secure" for us. It is already secure, as you stated, such that you are able to restrict who accesses the videos. So just passing around the link won't work if someone wants to share the video.
Obfuscating the link though doesn't seem to serve much purpose because the videos are already behind a login requirement. Even if they could predict the link it couldn't be downloaded without logging in.
I guess then you mainly want to stop students downloading the video and putting it somewhere where non paying people can get it. First point, after you turned off quicktime, you could play the MP4s. Yay, but there is no "download as" link on the flowplayer right click. So I think it is being played via HTML5, which does (at least on chrome) give you a "save as" option.
I write and use the PoodLL set of plugins. Part of its function is to provide an alternative to the standard multimedia plugins filter in Moodle. It does play MP4 via flowplayer out of the box. If you do use that, then the flowplayer will be used and that "save as" link won't show. However it is still pretty easy to download the file if you are a little savvy.
If you really want to secure it from downloading, you will need to work with a streaming server(Wowza) and the secure streaming plugin from Flowplayer. Basically what those links you posted are talking about.
I would not start by hacking a few lines of core Moodle, because it will be a pain to maintain and might be harder than you would think. I think you would be better to start with the RTMP plugin, and add all your logic in there.
You will no longer be using the Moodle file system. Instead you will need to store your videos somewhere the streaming server has access to them and use special links that point to them, eg rtmp://wowza.myinst.org/edvideos/gettingpaid.flv
That means that the videos will no longer behind Moodle's login wall, and that links could be passed around. But from the info on the docs you sent, perhaps that would be quite difficult. You should also check if those videos will play back on mobile devices, and if not whether that is a showstopper for your project.
Finally just to go way off on a tangent and cause head scratching. If you really want to secure it, you could can the whole mp4/flowplayer business altogether. I put together a few video tutorials/intros using sliderocket. I reasoned that rather than putting 15 sequential minutes into a single video, it would be better to integrate a menu connecting 5 or so shorter videos. So people could stop, rewind , jump to where they want etc. Since it is not a video file it can't be downloaded. Tada. Here are two links, but I suppose its a bit off base: