Kyle,
I think there are a range of options for implementing this, with varying degrees of flexibility and ease-of-use. One end of this spectrum is in fact already possible in Cantera. If you are using Cantera from C++, you can just write a subclass of GasKinetics which implements the getNetProductionRates method, and use an object of this type when setting up the reactor network. Of course, this method requires recompiling in order to switch mechanisms, and doesn't work with the Python or Matlab toolboxes.
A more flexible approach would be to introduce a Kinetics class where the rate-of-production function is specified as being implemented in a separate shared library, which the user can compile separately and choose at runtime. This approach could enable users to work with various existing reduced mechanisms that are implemented in this way.
A third option would be to figure out whether it is possible to write a generic implementation of the QSSA equations that is still reasonably efficient, in which case you could define the reduced mechanism without having to compile any code (and could even pair this with the code used to generate the QSSA mechanism in the first place if you wanted). This option is certainly the most complex to implement, but also probably the most interesting in terms of the capabilities that it provides.
Regards,
Ray