I don't have a particularly strong viewpoint on this, but I find it noteworthy that in your example the user themselves is asking for a specific version of the software. You don't seem to be intending for users to ask for simply the latest version and have that work, but a specific one, and you want that specific version to work exactly as it did whenever it was published.
I can see some instances in which this expectation is important, and others where it is likely not or else certainly less important than the security implications.
For the extremes, I see research using spaCy has a very strong interest in reproducibility and the impact of any security issues would likely be minimal on the whole simply due to the relatively few people likely to run into them.
On the other extreme, say some low-level dependency is somehow so compromised simply running the code will end up with the user ransomware'd after just-long-enough that this whole scenario is marginally plausible. Then say spaCy gets incorporated into some other project that goes up the chain a ways and ultimately ends up in LibreOffice. If all of these projects have pinned dependencies, there is now no way to quickly or reasonably create a safe LibreOffice update. It would require a rather large number of people to sequentially update their dependencies, and publish the new version, so that the next project up the chain can do the same. LibreOffice would remain compromised or at best unavailable until the whole chain finished, or else somebody found a way to remove the offending dependency without breaking LibreOffice.
I'm not sure how to best reconcile these two competing interests. I think it seems clear that both are important. Even more than that, a particular library might sit on both extremes simultaneously depending on how it is used.
The only solution - though a totally unrealistic and terrible one - that comes to mind is to write all code such that all dependencies can be removed without additional work and all dependent features would be automatically disabled. With a standardized listing of these feature-dependency pairs you could even develop more fine-grained workarounds for removal of any feature from any dependency.
The sheer scale of possible configurations this would create is utterly horrifying.
At any rate, your utter rejection of the article's point seems excessively extreme and even ultimately user-hostile. I can understand your point of view, particularly given the library you develop, however I think you should probably give some more thought to indirect users - ie users of programs that (perhaps ultimately) use spaCy. I don't know that it makes sense to practically change how you do anything, but I don't think the other viewpoint is as utterly wrongheaded as you seem to think.