By that logic, you don’t want to use any third party library. Even commercial stuff has the risk of being dropped tomorrow (see also: HHVM support in Symfony).
Zepto has been around for nearly 5 years at this point. I doubt it’s very likely it’s just going to drop off the face of the planet.
That said, the point of “you might not need jQuery” articles is less about avoiding it at all costs and more about not defaulting to it and mindlessly adding to every site you build. If you have a use-case that jQuery is the best tool for, then there’s not much reason to not use it, but like the saying goes, “if all you have is a hammer, all you see are nails.”
On a side note, don’t forget that if you a) don’t report the compatibility issues out to the browser maintainers and just silently allow libraries to cover them up, and b) don’t use projects other than jQuery, then nothing is ever going to change.