As mentioned you have to enable the CLR at the instance-level but you can enable it on the instance and add a DDL trigger FOR the DDL_ASSEMBLY_EVENTS event group in all databases where you want to prevent the creation of assemblies.

Something simple like this could do the trick:

CREATE TRIGGER [db_no_assembly] ON DATABASE

FOR DDL_ASSEMBLY_EVENTS

AS

BEGIN

RAISERROR('No CLR DDL activities allowed in this database.',11,1);

ROLLBACK;

END

GO