we have allowed linguistics to be turned into a discipline where simply describing 'the natural' is enough to ensure a nice doctorate degree that earns you the right to pass this idea onto the next generation of 'describers'

Describing nature is what researchers do in many branches of science, not just linguistics. I don't know why I even bother saying this, but for instance describing how people use language and how it evolves gives you keys to reconstructing ancient languages, understanding language acquisition is valuable in terms of teaching, etc.

How do I write to ensure that what I write now can be read in 20, 100, a thousand years time? Context?

Well... sorry to disappoint you but I'll answer 'yes'. There are some very accessible translations of the Divine Comedy, but if you don't know about the place and moment Dante lived you still miss half the ideas. Or Machiavelli. You know all the words he uses, but the kind of politics he talks about is completely alien to what is going on today. Do we forbid culture changes so future generations don't get confused, and technology changes so if they find old suff we built they don't need to think twice in order to use it?

We have the potential to make it so that everyone knows how to use the language, not just to have a large and accurate vocabulary but to actually understand how these words are constructed so that they can read and understand words on first encountering them, and even coin words according to the structure of the language such that anyone else would understand it too.

Personally I am not sure you can engineer a system that will allow for all future words and meanings to just fit in. And especially not a completely context-independent language that would be practical for humans to use. And force people to freeze language in a given state. And erase dialects by imposing one arbitrarily chosen standard dialect. Humans tend to not do that, and the examples of repressive language policies in history tend to not be pretty experiences.

Instead we're throwing our hands up and declaring that humans were meant to shit beneath a bush, probably always would do, and that it's arrogant to suggest there's a better way.

Or maybe it is because by fulfilling the immutability fantasy of those few who claim language changes are just like shitting beneath the bush we would lose more than we would gain and it isn't realistically a solution to any real problem?