I tried going the rendertexture route, but there were issues with getting and setting pixels from transparent textures. In the end I went back to doing regular GameObjects with low res sprites, and only round off the rigidbodies' positions and applying them to sprites. The same rounding happens on the camera.
If your resolution is off, you can get artifacting between sprites, but you can just set the window size using Screen.SetResolution(resX * multiplier, resY * multiplier). Any whole multiplication of 64 works just fine.
The benfit of doing it all this way, is that all your regular Unity skills still apply, unlike with drawing to a texture, which has its own pitfalls.