This is probably an accounting question, and you might be well advised to check with your auditors - they may want to adjust period end revenue with a provision for works started that won't be completed. But in principle, if the billing you can do is capped at 50% and the customer has decided to not continue with the work, you will have to back out the revenue you have recognised over and above the 50%.
I agree that the services team will feel hard done by as they have done the work in good faith - there's an argument to say that someone else should get the revenue adjustment (journal it to hit a different department).
From a business as a whole perspective, I'd be looking at ways to minimise risk of this happening again - 50-25-25 billing, or different penalties for customers backing out relating to actual effort expended (they would of course need to see evidence of the work completed, etc etc)