Chris, what do you mean by it's the first time you've heard of a properly diagnosed case of Mareks? Don't you regard the paralysis as diagnostic?
Mareks is transmitted in feather dander, so the clean-up has to be pretty thorough. It being a virus, does Virkon kill it? Off to find out. (Yes, apparently it does)
As far as I can find out, waterfowl do not carry it (they don't suffer from it).
Are your other chickens ill? Apparently the diarrhoea can be coccidiosis as Mareks damages the immune system and makes them more susceptible. If they survive, they may continue to excrete Mareks virus so infecting any unvaccinated birds you bring in.
So your options are to cull and start again. In which case do you buy vaccinated birds. If not, you rely on having cleaned it all away and not buying infected stock again. If you buy vaccinated stock then you should e able to keep any birds that survive from your current ones, since the vaccinated ones should be immune.