mordechai9
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It looks like everybody did a pretty good job of getting at this, but I thought I would just chip in my two cents with an alternative sort of answer.
First let's consider the throwing of the rock. Maybe you are familiar with the notion of a "free body diagram". Basically it just consists of a picture of the object in question, and arrows representing all the forces acting on the body. Now, if you draw a FBD of the rock when it's being thrown, this picture consists in the rock, and only the rock. In the picture, you will see a force arrow which represents the hand pushing on the rock. (You will also see an arrow pointing downwards representing gravity. Let's just ignore that for now.) Now at the same instant, if you draw a FBD of the hand (and only the hand), then you see an arrow of the same length, pointing in the opposite direction. This represents the rock pushing back on the hand. That's all that Newton's third law means.
If you do the same thing for the window and the rock at the initial point of impact, again, you will have a similar situation if you draw instantaneous pictures of the window or the rock. The window breaks because it is unable to sustain this force, which it feels in terms of a sudden, nonuniform increase in load. After the window shatters, the rock is no longer exerting a force on the window at all, so it is correct to say that there is not an equal and opposite reaction for a long time. The rock does not stop because the work done by the window is insufficient to fully dissipate the rock's kinetic energy.
Question: since the window is trying to push backwards against the flight of the rock, do you see bits of the window flying outwards, in the opposite direction? The answer is yes, I believe. However, the distribution of forces in the shattered glass is much more complicated, and it is not straightforward to predict the trajectories of the shards. Elastic and nonelastic deformation are complicated problems.