Why the Admiralty did not punish Thames Ironworks

Was Thames Ironworks allowed to go bankrupt because it had misbehaved as a naval contractor?

No. The Navy did not regard the yard as having misbehaved; its dispute was tied to Winston Churchill's political campaigns.

Thames Ironworks was not allowed to fail as an Admiralty warning to troublesome builders. It had not misbehaved from the Navy's perspective. Its offense was political: the company did not support Winston Churchill's campaigns. The distinction separates naval procurement discipline from the political circumstances surrounding the loss of a major battleship-capable yard.