A useful way to think about this is to consider existing human languages like English or mathematical notation. When you read these English words, it's like you're executing a program I've written that will change your brain state. A pattern in my brain is encoded, stored, and transmitted in a language that we've both learned in our own separate ways, then decoded to a pattern in your brain. But your brain is quite different from mine, and you're free to implement any sort of sandboxing you want against this information, and even against the language specification itself, in your own head. Erasing this barrier is equivalent to erasing individuality, so I think we ought to be able to do this for digital programs as well.
I hope that in the not too distant future, we will be able to design and manufacture custom hardware on a per-person basis. Because that's what it will take to preserve human autonomy and bodily integrity in the upcoming era of AI and brain augmentations. I don't want my neural interface to have a hardware-level backdoor (https://en.wikipedia.org/wiki/Intel_Management_Engine) like my desktop computer. There is also a bigger evolutionary problem behind this, and I expand more on that in this tangentially related past comment: https://news.ycombinator.com/item?id=49690354