It's time to remove Flash dependencies from your Office documents. Also, I'm pretty sure you can embed videos without using Flash Player.
Since you're at an inflection point anyway, I'd recommend taking a minute to think carefully about not just what distribution format is most convenient for you, but what's most useful for your audience and the variety of devices that they might want to consume your content from. I'm skeptical about the optimality of embedding videos in other documents for most use-cases (although I totally get embedding a video in your slide deck in the context of a live lecture).
Also, Flash Player has been blocked in current versions of Office for a long time. I think you can jump through hoops to enable it, but I wouldn't expect that support to remain in future versions. We don't interact with the Office team much, but I imagine that they piggyback on IE for access to the ActiveX player, and when broad support for Flash Player is removed from Windows 8 and higher later this year, it's reasonable to assume that the facilities available to Office for playback will also go away.
In terms of the Standalone player, it will work until a breaking change to the underlying Windows APIs renders the standalone player unusable. That's a matter of when, not if. Much of the work we do is the invisible work of keeping up with the latest operating system and browser changes. That work is no longer happening, unless your organization wants to license a maintained copy of Flash Player through HARMAN. In the context of a handful of lesson plans, it would be far more cost-effective to recreate them in modern technologies.