I decided to run a "check" at startup that would try to determine if the SQL instance had been cloned.

TLDR: Hard-code the SQL host machine name and domain in a stored proc and compare those values to SERVERPROPERTY(N'MachineName') and DEFAULT_DOMAIN(). Do something drastic if the values don't match.

If anyone is interested, I blogged about it: SQL Server: Attack Of The Clones