It will change things too, not for reddit, but for competitors (like kbin).
A tiny site can only grow so fast, at some point things start breaking (both technically and as a community) and users stop joining, but as sites grow bigger they also gain the ability to grow faster.
The protest means that every possible alternative to reddit has been growing as fast as it can reasonably support. That's probably not fast enough to hurt reddit this time, but next time it might be.