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