Really the shruthi-1 control board is just a microcontroler with a an lcd screen, midi, some buttons, pots and two connectors to the lower pcb. With the right firmware it could work similiar to the ambika control board where the cards are stand alone synths.
you probably are right about that... so you could use that to manage the MIDI and controls, and make a PCB that does all the sound. Actually the good thing is that the AVR would not have to generate any audio, since that would be done by the SID (or swinsid)
Btw. I think it's great that you are using SwinSIDs! Too many C64 get stripped of their SID chips for projects like the SammichSID, often fully working ones... and it's a pity.