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Programming languages exist today because computers can't handle ambiguity and don't understand software design. In another 50 years, machines will be a lot smarter, more able to handle ambiguity, and better than people at designing workflows and catching potential errors. Like the horse, no doubt some people will still prefer to do things the old way, but there's a good chance this will be limited mostly to academic exercises.
All they're saying here is that the tools we have will progress a lot in the next 50 years. There are some obvious problems with the way we design software right now which are due to human limitations. The only way to fix those is to remove a lot of direct control from humans and give it to AI programmers. Manually writing JavaScript in 2066 will be like manually carving arrowheads today: still effective but not something you would do for a serious purpose.
EDIT: That said, I do think this is a cute idea.
1- We only need secure multi-party computation algorithm if we cannot trust the server. In cases that server can be trusted with behavioral fingerprints then we can use server to to do the comparison.
2- One can assume that in some cases the server should not know about the behavioral fingerprint. For example in case that this procedure is implemented as a service, it might not be proper to send client side mouse movement and key presses to the server. Still server can be trusted as a mediator but should not know anything more than fingerprints being almost equal. You are right that behavioral finger prints like mouse movement are fuzzy. Specially since agent and browser are running on two different threads they get different time stamps for each mouse location. In this case you have to introduce some acceptance for fuzziness as you mentioned. Some statistical comparison. This is not as easy as checking equality securely (like Socialist millionaires problem) but you can in theory turn any circuit and make it secure so that the circuit will only expose fuzzy equality and nothing more about the data. See secure multi party computation: https://en.wikipedia.org/wiki/Secure_multi-party_computation
But your concern is valid since in practice the computation involved to do secure multi party computation in this case might be demanding for a browser. I have yet to verify that in practice. Keep in mind that our case is a bit more relaxed than general secure multi party computation problem since we have a server that can be trusted a little bit. Maybe that can help us a bit in devising a secure computation scheme. Any volunteers to work on that? :)