use of CLR makes it harder for a SQL Server administrator to see what's going on with their SQL Server.
Yes, Agreed! However, I've recently started using NET Reflector with an add-in that allows you to see the source of all the CLR routines currently in the database.
http://www.denisbauer.com/NETTools/SQL2005Browser.aspx
It is a joy to use and it means that the D**ned developers can't hide their code from you, particularly as you can decompile it into VB or C#. and save the source to a file. Power to the DBA!
Best wishes,
Phil Factor