I don’t know exactly what Saitou (or the manga’s author) intends; but there are three involved characters (copied from “places and names”):
- 斉藤 英二郎 (さいとう えいじろう): the main character. He is an idealist who wants to be a doctor to help people as opposed to become rich.
- 春日部 一郎（かすかべ いちろう）: nicknamed “God’s hands”, is a professor at the Eiroku University hospital that just do initial incisions, and otherwise is interested only in study of eels.
- 白鳥 貴久（しらとり たかひさ）: doctor at the 1st surgery department that did the actual operation (Ep.2) at which “God’s hands” appeared. He is the instructor of Saitou and Dekune.
The professor giving instructions to do the operation, knowing it would be useless, but doing it to get money from the patient family, is 春日部 一郎.
The one that did the actual operation, and that then reveals the futility of it, is 白鳥貴久.
When the operation has been done, Saitou didn’t knew about the ugly side of it, so he couldn’t have disobeyed.
The word 指示 has been used by Shiratori to tell why the operation had been done; “教授の指示だ” B of page 14. So that professor is Kasukabe.
Saitou laments someone (non stated) didn’t disobeyed the “instructions of the professor”. As the professor in the previously said “教授の指示だ” is Kasukabe, then the conclusion of Jonapedia is that the meaning is that Saitou is mad that Shiratori didn’t disobeyed those instructions (at first I had understood it like you; but indeed Jonapedia interpretation is the right one; just after that, Saitou says 僕も同じだ, I am the same (so if he is “the same” he also another one (yes, it’s paradoxical ) than the subject of the previous sentence.
And the next one (I haven’t looked if it has already analyzed, but I read it on the manga), says Me also,… I didn’t contradict a single word against Pr. Shiratori (crudely worded, as I haven’t correctly analyzed the sentence yet); so as Saitou now says that, he too, didn’t disobey his superior, it’s another indication that the previous sentences is about Shiratori not disobeying his own superior; hence “ぼくもおなじだ”