I think the biggest reason not to allow encrypted data is the second point you mentioned. The bands will begin being used for purposes other than what the rules of ham radio allow.

There are some individuals apart of groups who would definitely use encryption on the ham bands as a means to have communications taking place that are not allowed by the rules. The biggest one would be communications with a connection to politics. Met plenty of these types who are jealous of the ham band and scorn the rules because of that, so they keep themselves on CB and FMRS.

Also like you mentioned, it is now free radio space for commercial entities to try to use.