I’m not quite sure how easy it will be with sonic-pi to make the MIDI and audio connections, but in general I think the problem will be getting (sonic-pi) programs to run directly (just by uploading).
For simple programs this may work, as the autorouter will automatically connect the MIDI and audio connections. But with complex setups this might be more difficult.
Probably it depends on a test. The best thing will be to just start and run only sonic-pi with a default program. Then you can think about how to organize the programs as sound patches and how to get them into Zynthian.
It will be interesting if you have programs that should play loops, synced to MIDI clock, load samples, use multiple MIDI interfaces etc.
Regards, Holger