Josh Marshall hits the nail on the head:
Every non-hard-right congressional Republican will have this episode in mind going forward the next year -- it will shape votes, positions on key issues. And what happened in this race will be the backdrop for every primary contest between a mainline and hard-right Republican this cycle -- think particularly of the Crist/Rubio contest in Florida, which hard-right Republicans are already pointing to as the logical place to repeat the Scozzafava/Hoffman pattern.
This is the electoral equivalent of those brief moments earlier this year when prominent Republicans issued tepid criticisms of Rush Limbaugh only to be forced into craven apologies hours or days later. The hard-right of the GOP just got a much stronger lock on the institutional Republican party than it had before. And, let's face it: the lock was pretty strong to start with.