Rich Harris actually disagrees with the browser vendors decision to deprecate alerts. From the article you linked:
> We can't normalise the attitude that collateral damage is the price of progress, even if we accept the premise — which I don't — that removing APIs like alert represents progress. For all its flaws, the web is generally agreed to be a stable platform, where investments made today will stand the test of time. A world in which websites are treated as inherently transient objects, where APIs we commonly rely on today could be cast aside as unwanted baggage by tomorrow's spec wranglers, is a world in which the web has already lost.
> We can't normalise the attitude that collateral damage is the price of progress, even if we accept the premise — which I don't — that removing APIs like alert represents progress. For all its flaws, the web is generally agreed to be a stable platform, where investments made today will stand the test of time. A world in which websites are treated as inherently transient objects, where APIs we commonly rely on today could be cast aside as unwanted baggage by tomorrow's spec wranglers, is a world in which the web has already lost.