Swapping two 500kohm pots with one MCP42010 10k ohm digital pot
It would most likely be fine to use a 10k digital pot in replacement for the 500k pots. There are a few gotchas when working with digital pots, the first one is they can't take a lot of current (only 1mA for the wiper current of this part) through them or they burn out. In this case you should be fine because the input of the 556 is high impedance and takes very little current, the cap is also high impedance at DC and also takes little current. 

You may want to use a 100k part instead of a 10k part, to get the same resistance range, otherwise you might want to increase the cap by a factor of 10 to get the same RC time constant range. 

The other problem is the resolution, with only 256 taps, this limits the frequencies that can be generated. A regular pot is continuous and can generate as many frequencies as you want with the RC filter of the 556 timer. A digital pot will restrict this to whatever the pot can handle.