POSIX time is great for most of the uses to which it is put. There is no need to get rid of it any time soon, nor could we. It just shouldn't be used as the basis of anything requiring sub-second accuracy, linearity, or precision.
This failure in particular would not have occurred if the kernel and all the pertinent applications used a reliable time base do timing with, instead of trying to derive reliable timing from a time base with all the stability of a drunken sailor.