The gemara (Brachos 5b) writes that negaim are yisurim shel ahavah in Bavel but not in Eretz Yisrael. Rashi explains that in Eretz Yisrael the affliction of negaim was more severe because the leper had to be send out of his home in a walled city; in Bavel where there is no kedushas ha’aretz a leper could stay at home. Tosfos disagrees, as the gemara (Archin 29) tells us that the law of batei arei chomah (walled cities) was not in effect once the count of yoveil ceased, meaning there was no longer a kedushah to the walled cities (see Rashash). Certainly by the days of R’ Yochanan the yoveil was no longer being counted and the law of shiluach machaneh was not in effect even in Eretz Yisrael. Tosfos explains the gemara to mean that negaim in Eretz Yisrael were a more severe punishment because the laws of taharos were more strictly observed there than in Bavel.
The Tzla”ch offers a novel defense of Rashi. Although the kedusha of walled cities was no longer in effect without a yoveil count, Yerushalayim has an additional level of kedusha because it was the makom Shechina, and a leper would have to move outside its city walls. The simplest proof to this contention is that the parsha of metzora was given in the desert (and practiced there, as we see from the episode with Miriam) before the conquest of Eretz Yisrael and before the yoveil count ever started. Since the desert camp surrounded the Mishkan, it had the kedusha of makom mikdash. Furthermore, the Rambam (Bias Mikdash 3:8) writes that a leper who enters a walled city violates the mitzvas aseh of “badad yeishev m’chutz lamachaneh”, but if he enters the boundaries of Yerushalayim it violates a lav as well. Even though the kedusha of arei chomah was not in effect when R' Yochanan lived, the law of metzora still was practiced with respect to Yerushalayim.