I
The Torah requires one declared to be tomei as a metzora to wear torn clothing, let his hair grow, and cover his head (Vayikra 13:45). The Talmud (Moed Kattan, beginning of the third chapter) understands the idea behind these requirements is that the metzora must observe aveilus (mourning). Our tradition has it that a nega tzoraas is a supernatural punishment for having violated certain specific sins (Erchin 16a), and one who is a metzora is in a certain sense compared to one who is dead (Nedraim 64b; Berachos 25a). The halacha usually requires that the surviving relatives of a deceased observe aveilus. Here, because we assume that the metzora himself is responsible for his status of being considered "dead", we require him to observe aveilus over his own "death".
We have a similar idea regarding one put in "cherem". A cherem is a curse given by a beis din to a sinner that he should die. The Talmud points out (Moed Kattan 17a) that the three letters of the word "cherem" correspond to the ramach eivorim (248 parts) in the male body, implying that the cheren/curse is intended to effect all the 248 parts of the sinner's body, and thereby cause his death. One who dies while in cherem is considered like one who was put to death by the beis din, and his family may not observe aveilus (Shulchan Aruch Yoreh Deah chap. 345:4-5). Because the sinner (who was put into cherem) was the cause of his becoming like a "dead person", we therefore require him to observe aveilus over his own "death".
One who sinned and was sentenced to death by a beis din of twenty three dayanim is considered (in a certain sense) as if he were already a "dead man" even before his execution[1]. Similarly, when the beis din declares that one is in cherem, and when the Kohein declares the metzora to be "tomei", they too have the special status of being partially considered a "gavra ketilla".
The chumash tells us (Breishis 7:4) that when G-d finally decided to destroy all of mankind with the mabul, he waited seven days and only then caused the mabul to begin. According to our mesorah, Hashme's waiting seven days represents the fact that He observed a mourning period (shiva) for mankind. The commentaries point out that it is very strange to observe aveilus before the person dies just because he is about to die. The generally accepted understanding of this is that once G-d has declared (as a beis din) a death sentence on an individual (or on mankind), that person is now already considered partially a "gavra ketilla", and there is already room to begin observing aveilus just as there is in the case of one put into cherem.
II
Despite the fact that it is a mitzvah for a kohein to declare a metzora as a "tomei" if his conditions warrant doing so, this is no longer practiced today. The Chofetz Chaim (Shemiras Halashon, Shaar 1 chapter 6) suggests that perhaps the reason for this inaction is the following: since we no longer have a beis hamikdash and can not bring korbanos, and as such would not be able to complete the tahara process once the tzoraas clears up, we have no right in the first place to declare the individual tomei. The Talmud (Nazir 61a) establishes that a non-Jew can not be mekabel tumah because if he would become tamei he would not be able to become tahor. True, an earthenware vessel (a kli cheres) can be mekabeil tumah, despite the fact it has no taharah bemikveh. But with respect to people becoming tamei the rule is that only one who can later purify himself from the tumah is able to become tamei. Purifying oneself from tuma represents the idea of teshuva (repentance)[2]. We only punish the sinner by declaring him to be a living "gavra ketilla" if we see a chance for him to do teshuva.
The Talmud (Yevamos 90b) and the Shulchan Aruch quote from the Megillas Taanis the tradition that beis din has the right to punish people, even with death or with lashes (malkos), despite the fact that the halacha doesn't dictate this punishment, provided that a) it is only a temporary measure and b) the beis din asses the situation and feels that much will be gained - either for the individual or for the community - by this punishment being administered. One could perhaps understand that it might be permissible to throw stones at those driving cars on Shabbos if it would seem that we will thereby a) encourage the drivers to become Sabbath observant or b) prevent others in the community from being mechaleil Shabbos. But if we really do not think either of these goals will be accomplished, and the only result we can foresee is that those who are non-observant will simply become more anti-religious, then clearly there was no hetter to throw the stones in the first place[3].
[1] See Chidushei haGriz al haRambam Hilchos Rotzeach
[2] See Mipeninei Harav, Parshas Shemini
[3] See Eretz haTzvi p. 266