This is a difficult question and is discussed at length by the Mefarshim.

1. The Mishnah in Gitin (54b) discusses a case similar to yours. The Mishnah states that a Kohen in the Beis ha'Mikdash who deliberately did "Pigul" (he had in mind at the time of slaughtering or sprinkling of the blood of the Korban that he would eat the Korban at the wrong time) is obligated to pay.

2. The case of the Mishnah in Gitin is not quite the same as the case of the Mishnah in Zevachim (2a), because in Gitin the Korban is invalid, while in Zevachim the Korban is valid. However, Rashi in Bava Kama (5a, DH u'Mefagel) discusses your case. The Gemara there (Bava Kama 4b) states that according to Rebbi Chiya, there are 24 primary categories of damages. Rebbi Chiya does not mention Mefagel (the aforementioned Pigul case) as one of the categories. The Gemara there (5a) says that the reason why he omits Mefagel is that he is not discussing Kodshim. We see from there that, in principle, one would be liable for Mefagel. Rashi writes that Mefagel refers to a Kohen who slaughtered the Chatas of a Yisrael with intent that it should be a Shelamim. The Korban does not exempt the owner from his obligation and he must bring another one. According to Rashi, the answer to your question is that the Kohen is obligated to pay for the replacement Korban. However, Rashi does not tell us explicitly whether this applies even in a case in which the Kohen did this unintentionally.

3. However, the Shitah Mekubetzes in Bava Kama in the name of the Tosfos ha'Rosh writes that the reason why Rashi there explains that Mefagel means that the Kohen had the wrong type of Korban in mind, and does not explain it according to the normal meaning of Mefagel -- that the Kohen intended to eat the Korban at the wrong time, is that one might have thought that since there are many different types of Korbanos in the courtyard of the Beis ha'Mikdash at any given time, the Kohen might be considered "Anus": he is not to blame for not remembering which type of Korban he is supposed to be offering. Therefore, Rashi chooses this example to teach that the Kohen nevertheless is liable because of the principle that "Adam Mu'ad l'Olam" -- a person who commits damage with his person is always considered to be at fault and must pay. Accordingly, even if the Kohen acted unintentionally, he still must pay.

4. If the Korban which the Yisrael wanted to bring was a voluntary offering, it is possible that the Kohen does not have to pay, because the Yisrael's intention was to bring a present to the Beis ha'Mikdash, and in effect he fulfilled his intention, even though the Kohen's intentions were not precisely what he wished. (See Mishneh l'Melech, Hilchos Chovel u'Mazik 7:4.)

Certainly, this is a rather complex subject, and so far we have only touched the surface of it and surveyed briefly some of the sources.

Kol Tuv,

Dovid Bloom