Mixed Signal Grounding: Which approach will yield better isolation and analog performance?
I don't like (2) very much from a CAD perspective because then you can't have separate nets for AGND and DGND.


In Altium you can use a component called a "net tie" to physically connect two nets in a layout without actually merging the two nets into one. Other CAD tools may provide similar capabilities.


  Is there some reason not to go with (1), in terms of noise performance? 


Your option (1) forces the return currents for the digital signals to find a long path back from load to source. This means the complete signalling circuit will encompass a relatively large loop, which can result in coupling to other circuit loops and/or emissions.


  Is there a better way to keep the digital noise away from my precious analog circuits?


Your option (2) is one way.

You could also provide a capacitive path between the two ground nets near where the digital signals cross. However this can still cause some crosstalk between the digital signals due to the shared constricted return path.

You could also use an isolating device such as an optocoupler or transformer to carry each digital signal across the gap between the two ground planes. Normally, due to cost, you'd only use this technique if you need to allow for substantial voltage difference between the two ground nets.