I am not sure it is really 2 sources of power, both come from the main house. You are allowed up to 6 disconnects. The only issue I see is they have to be grouped. The exception George pointed out in his first answer clearly says "3 and 4 way switch loop". The trick is getting the 3 way close enough to the sub panel to be grouped and still be useful as the light switch. That is why I suggested a 2 pole in the travelers at the point on entrance marked disconnect and the 3 way where you need it. That is still pretty ugly because most people would assume it was a 4 way.
If you go the other way, I agree with Harold, I would label the switch. I do have a situation in my house I know is not legal but it is well labeled and "come and get me copper". I have a separate receptacle circuit, fed from the main panel in the garage next to the sub panel in my house. It is just so I will have light if I am working on the house power with the feeder turned off in the garage. It was actually the original circuit that fed the garage before I flipped everything on a service upgrade.
It has a red cover and a label saying it is "fed from the garage".