SQL CLR very slow on Amazon EC2 Instance (SQL Server 2014 CU6)
It turns out that the CLR was not enabled and for some reason the exception wasn't being trapped and SQL Server took about 15 seconds just to say that the CLR was not enabled but during that time the instance is being kept at 100% CPU and hogged down.

In case anyone happens to have the same problem, you can turn the CLR on by running this:

sp_configure 'clr enabled', 1
GO
RECONFIGURE
GO