Except that proprietary voice codices are allowed :(
These protections are to ensure the FCC / government are always able to decode amateur transmissions. These aren't protections for the operators themselves.
I completely agree with your sentiments though, the amateur bands should not allow proprietary commercialization.
At least with a proprietary codec with that patent restriction anyone can still go out and buy a compatible radio and jump right on. And if the improvement to capabilities is large enough the trade off is worth it. It's not ideal but it's much better than allowing encryption where the transmissions aren't accessible to anyone by design.
Which is not a small mount of money, but isn't that bad given that most amateur radios (excluding the recent Chinese models) retail for ~$500, and commercial radios retail for $1,000+.
That said, I'm pretty sure everyone would prefer to move to Codec2, but the lack of hardware offerings is a problem. I'm looking forward to the day the first real SDR handheld transceiver comes out so this can be implemented by the open source radio community. It's clear that none of the radio manufacturers are interested in interoperability, much less adopting community standards.
§97.113 Prohibited transmissions. (a) no amateur shall transmit (4) Music using a phone emission except as specifically provided elsewhere in this section; communications intended to facilitate a criminal act; messages encoded for the purpose of obscuring their meaning, except as otherwise provided herein; obscene or indecent words or language; or false or deceptive messages, signals or identification.
(§97.207 outlines the space station exception)
While it doesn't call out encryption by name it more broadly prohibits "messages encoded for the purpose of obscuring their meaning." I take that to include both encryption and obfuscation methods like steganography.
If done properly and using a sequence that only you understand, it is possible to become completely invisible to interception for most practical situations. Someone with RF monitoring equipment could determine the source of broadband emissions, but without actually investigating the design of the physical transmitter they wouldn't ever know conclusively what is happening. This is why the FCC requires you publish the algorithm of the PRNG which modulates the data into the final DSSS signal. If you never do this and take decent measures to ensure your sequence appears as pure noise (simply encrypting your payload would do this), there is little anyone could hope to do to discover your presence if they were listening in the middle.