How to disable 40k contacts from GUID

Hello All,

I have complicated SQL query that gives me 40,000 contacts records,that I have to disable 40,000.

For contact specific I am using GUID to disable contact.I can't converted SQL query into fetch xml or query expression.So,I plan to do this by calling custom work flow with passing a parameter of GUID from external .net application. 

please suggest me the correct way.