Similarly, you could argue that when someone sends a movie to your home to watch over cable, you could do anything you want with a dvr recording of it. But we know that's not an argument that actually holds any water, legally or ethically.
Merely reading a news article is certainly non-commercial, so by the analogy you proposed I believe this JavaScript workaround is entirely legal.
In this case, you're taking content that you haven't paid for, and violating the terms it's distributed under by disabling some portions so you can consume it without paying.
I'd argue that's closer to disabling macrovision on a VHS tape so you can make a backup copy of a rental tape to keep for yourself, and I'm pretty sure that's verboten.
That's like saying the cops can use heat-sensors to look at houses, because thats just electromagnetic signal and you can render it however you want. No invasion of privacy there right?
I would argue that since the NYT is willfully delivering you the content of an article and merely instructing your browser to conceal it, that's a far cry from "trying to 'lock' their door." If someone was distributing their username/password or an authorized cookie, or using a server-side exploit to access content, then I think that would constitute a breach of ethics if not law.
Basically, my point is that once the NYT willfully transmits data to your computer, you should be able to manipulate it any way you wish, obviously barring any sort of commercial use or redistribution that violates copyright laws. Anyway, it's not that hard to protect data from certain users and make it available to others. That's a design pattern as old as multi-user computer systems/networks.
When you make a web request to the NYT servers, they are willfully distributing a copy of that content to you. Obviously, you're not allowed to do anything you want with the content (like sell or otherwise redistribute it), but I certainly think you can manipulate it and view it any way you want.