What I would do is disconnect the coolant hoses at the bottom part of the oil filter housing, and allow coolant to drain out of there into a clean container. That will get about 3.5L out, and should put the coolant level below the water pump.
Then do the timing belt job including replacing the water pump.
Put the coolant that you drained out back in, make sure the car is running, and nothing is leaking, etc. Leave it that way for a day or two while you make sure there are no problems like a leaking water pump.
By doing this, you'll make sure the system isn't going to leak before you put in the new coolant.
At that point, you can drain the old stuff again, and this time also drain the radiator. Remove the thermostat and put the thermostat housing back with nothing in it, so you'll get full coolant flow through the system. Put in ordinary tap water, run the engine for a few minutes, drain it, fill it, and repeat this a couple times. That should get all the old stuff out.
If you want to get all the tap water out, you could consider wasting 6L of distilled water by doing your last flush with it.
After you're satisfied that you've flushed it enough times, drain the water out, put in the new thermostat, and fill it with the new coolant/distilled water mixture.
