The first of those meanings is the only one that is used. The stones that are thrown are presumed by most people to be thrown at someone else, outside of the house, as an attack. And the reason it's such a bad idea is then obvious: retaliation in kind will result in the destruction of your home. You shouldn't attack when you are vulnerable.
The sense of 'hypocrisy' arises I think because the saying could be used in this context: "Don't start a fight in an area in which you are vulnerable". Don't make fun of someone's speling when they can then turn around and say "You can't even spell 'spelling'." This conveys the sense that you shouldn't criticize others for weaknesses that you share yourself. Not, however, because it's hypocritical, but because it is strategically weak: it is a poor choice of territory on which to fight. Don't start a fight in a swimming pool, if you don't know how to swim. The proverb doesn't suggest moral self-contradiction, or the creation of a rule by which the rule-maker could himself be convicted: it is strategic advice given with ironic intent, not moral judgment.