Since they didn't mention even an estimate of the server costs, it's safe to say that it's probably not large enough to cause a stir over, at least in comparison to the cost of what they'd charge for using their CSS and other front-end code.
They could've just denied access to the assets so that the AJ webdevs would have to recopy-refix them, while at the same time continuing the legal press. A couple of weeks is not a long time when going through the legal system.
I'm not saying that winning a lawsuit is the ideal situation. I'm saying it leaves open the possibility that someone with actual power at AJ notices the problem, gets things fixed, and says, "Hey, this is a cool product, can we talk about a long-term deal for future stories?".
Now they not have virtually no chance in getting AJ as a customer, which is too bad because AJ actually has money for these kinds of deals. But even if scrollytelling didn't want to work with AJ out of principle, they've now unnecessarily turned off other big media clients. Big media clients, i.e. traditional outlets with the morals, lawyers, and funds to pay for proper distribution contracts. These companies generally have lawyers who do not like dealing with vendors who litigate over Twitter.