You cannot use 9v with MCP41XXX powered by 5V. The datasheet specifies voltage range on resistor terminals as 0~VDD, i.e. up to 5V in your case.
The only option I can think of is to make analog part also 5V, and then add 9V powered amplifier stage on the output.
Here, I rearranged your analog part for you. Frankly, I have no idea what it does. I am not an analog guy, but even I know that there should be output somewhere. Also, the polarity of C1 seems to be wrong.
Those 8V from the diode enter circuit through fairly large resistor. Plus, all ground connections also have large resistors in them. IMHO, this circuit should not be sensitive to supply voltage at all.
Since you figured out your analog part can work from 5V supply, your suggested supply #2 should work just fine if you remove R19.
Note, that digital potentiometers are digital devices and their resistor terminals are technically not isolated in any way from digital circuitry. So, any tinkering with GND won't do you any good. The best your can do is place all analog parts over separate part of ground plane, making sure it is connected to digital part in one place only. Since MCP41010 will be powered from digital part, you can make separation line passing under the chips around resistor terminals.
BTW, dual chip MCP42010 would be much better choice. It has more convenient location of the resistor pins - all 6 on one side of a chip. And you only need 3 of them instead of 5.