I didn't get the impression from that article that "replace the native implementation with a JavaScript implementation for better performance" was the goal at all. Rather, the goal seems to be "move away from a situation where one holdout browser (traditionally IE, more recently Safari/iOS) could scupper a new feature completely, and toward one where holdouts are just slower if they don't support that feature natively". There have been lots of examples of that strategy working - jQuery/QSA, asm.js etc.
Is that a misleading impression? Does Houdini have another agenda not covered by the article?