There are three opinions here:

1) The opinion of Rabanan, in Sanhedrin 79a, is that if A intended to kill B, but instead killed C, he is liable to the capital penalty, because he was intending to kill.

2) The opinion of Rebbi there is that in the above scenario, A is exempt from the capital penalty, since he did not kill the person he intended to kill. However, Rebbi adds that since he is exempt from the capital penalty, it follows that he has to pay for the financial damage that was done. Therefore, he has to pay the monetary value of the woman who was inadvertently killed (b'Shogeg).

3) The opinions of Rebbi and Rabanan are relating specifically to cases of murder. The Shitah of Rebbi Yochanan is a third opinion and is not necessarily related to a scenario involving murder. It could be that somebody slaughtered a stolen cow b'Shogeg on Shabbos. He is liable to the capital penalty for breaking Shabbos, and even though he would not actually receive this punishment since he was only Shogeg, nevertheless Rebbi Yochanan maintains that since the transgression has the severity of a capital crime when done deliberately, it follows that he is exempt from payment even though it was done inadvertently.

As far as I am aware, we do not know what Rebbi Yochanan holds about the dispute between Rebbi and the Rabanan (above (1) and (2)). Probably, since Rebbi Yochanan is an Amora, he would not take sides in an argument between Rebbi and Rabanan, who are Tana'im. However, Tosfos points out that there is a different reason why Rebbi Yochanan would not agree with Rebbi's Halachah about paying money for the value of the murdered woman. This is because Rebbi Yochanan maintains that one is exempt for paying money for any capital crime commited b'Shogeg, whether it is murder or Shabbos or anything else.

Kol Tuv,

Dovid Bloom

1) Yes, I think that it is correct.

We do actually sometimes find that Rebbi Yochanan does not seem to accept the Mishnah. See Beitzah, beginning of 12b, where Rebbi Yochanan said that "Hav'arah and Bishul is not a Mishnah." Rashi there (DH Einah Mishnah" writes that this Mishnah was never taught in the Beis ha'Midrash.

(See also Tosfos to Beitzah 33b, DH Patur, who writes that it is obvious to Rav Kahana that the Beraisa was mistakenly taught (however, Tosfos there is referring to a Beraisa, not a Mishnah).)

However, I think it is unusual that Rebbi Yochanan does not accept a Mishnah, so that is why Tosfos writes that Rebbi Yochanan does not agree with the stam Mishnah here.

(Even though we do sometimes find that Rebbi Yochanan might say that the Halachah does not follow a certain Mishnah -- see, for instance, Shabbos 61a -- this is unuusal, so Tosfos here assumes that Rebbi Yochanan does not argue.)

2) I was thinking about this again, and I remembered that there are a few sources that suggest that Rebbi Yochanan was very close to being on the level of a Tana, so I think that indeed Tosfos is stating that, nevertheless, Rebbi Yochanan is not actually a Tana and would not disagree with the Stam Mishnah here.

a) See Yoma 43b, where Rebbi Yochanan did not listen to the Tana. See Chulin 82a, where Rebbi Yochanan said that Paras Chatas is not a Mishnah. Rashi there writes that it was not stated in our Mishnah. We can add these sources to Beitzah 12b and Shabbos 61a that I cited above.

b) See Chidushei ha'Ramban to Shabbos 114b, who says that one can say that Rebbi Yochanan was a Tana and can argue on the Beraisa. See also Me'iri to Yevamos 7b (page 32 in the standard edition of the Me'iri, DH v'Achronei), who writes that Rebbi Yochanan lived at the very end of the period of the Tana'im and is capable of disagreeing with a Beraisa. (The Ramban and Me'iri write that Rebbi Yochanan can argue with a Beraisa but they do not actually say that he can argue with a Mishnah.)

c) However, it seems that Tosfos does not agree with the Ramban and Me'iri on this. Tosfos (Kesuvos 8a, DH Rav) writes that Rebbi Yochanan is an Amora, not a Tana. I found, bs'd, some more places in Tosfos that seem to be consistent with what he writes in Kesuvos 8a. These are Tosfos to Yevamos 7b (DH Rebbi Yochanan), who says that Rebbi Yochanan is not a Tana, and Tosfos to Shabbos 61a (DH d'Avad), who writes that the Beraisa does not argue with Rebbi Yochanan and Rebbi Yochanan does not argue with the Beraisa. See also Tosfos to Nidah 56b (DH Amora'ei) who understands that it is obvious that Rebbi Yochanan would not argue with the Mishnah.

d) I think that we now van add our Tosfos in Chagigah who is stressing that Rebbi Yochanan would not argue with the Stam Mishnah. This fits with the Shitah of Tosfos in other places that Rebbi Yochanan is an Amora, not a Tana.

Kol Tuv,

Dovid Bloom