In almost a decade of using Clojure, I've never seen persistent data structures become the bottleneck. The difference in cost is O(1) for in place mutation vs O(log 32 n) for revisioning. Note that the large exponent means the tree ends up being very flat, so updates end up being quite cheap in practice. Most times when I do something to a persistent data structure, I only change a small portion of the overall data structure. In fact, I think it's quite rare that you'd end up cloning the whole thing.
Personally, I view mutability as an optimization, and I think it should be used in cases where you actually need the performance beyond what persistent data structures can offer. My experience is that such cases are far and few between.
From user perspective, you're effectively making a copy each time you make a change, but you're not paying the price of a full copy. Instead, the cost of updates tends to be o( log n) vs o(1), which turns out to be fast enough for vast majority of cases. You can read about this in more detail here: https://en.wikipedia.org/wiki/Persistent_data_structure
JavaScript has a number of libraries that implement these data structures, underscore.js and immutable.js are examples. However, these libraries still require a lot of programmer discipline to use. For example, nothing stops you from putting a mutable object into an immutable data structure. At that point all bets are off.
There are also languages that are built around the idea of immutability. For example, I work with ClojureScript, and all data there is immutable by default. Data structure syntax in ClojureScript is actually quite similar to JSON, and it makes it easy to move between the two.
edit: seems like you updated as i posted. i’m just trying to understand how you do this without using an object. you mention use of a map, but that is also an object. also, by copying a map i still access the original values, which is specifically what this article is implemented to avoid? i may be over my head here, i’m just trying to understand the “correct” way of doing this in javascript.