What comes to mind that might work would be to layer on (and eventually migrate to) a database-managed system.
As an approach it's not necessarily super easy, but it's also not impossible or beyond the reach. FileMaker is actually a pretty good / easy-to-learn system for this kind of stuff.
There's a TROI plugin for it that handles metadata. Even better (if you have the patience) is to build your own metadata integration using something like exiftool (an open source command line app, very powerful) which, with a little jujitsu, integrates with FMP very nicely.
Process would go something like this:
Database that includes a "Photos" table.
From each photo you extract a list of all associated keywords
Each new keyword is added to a "Keywords" table in the same database. Any duplicate keyword is not added.
Each item in the Photos table "knows" its associated keywords by means of a reference to the Keywords table.
The icing on the cake would be to not only extract but also push-to-update those keywords into the IPTC metadata of each individual photo in such a way that PM continues to recognize them -- so you use both your custom solution and PM seamlessly with each other.
All that assumes you even need embedded keywords. If the point is to coordinate how images are presented on a web page or how they appear in web searches, you might be able to forego the IPTC data altogether and handle everything via database + dynamic web pages with keywords attached.
It can take a while to figure out the best approach, but it sounds like you're doing cool stuff.