In the sentence "を食べるのは、彼だ," the use of "のは" is correct and commonly used to emphasize that the action of eating is associated with "彼" (he).
If you change it to "を食べるのが、彼だ," it slightly alters the nuance. Using "のが" instead of "のは" would place more emphasis on the action itself being the subject, rather than the overall statement.
"を食べるのは、彼だ。" → The focus is on the fact that he is the one who eats.
"を食べるのが、彼だ。" → The focus shifts to the act of eating, identifying he as the one doing it.
While both can be used, "のは" is more natural in this context because it emphasizes the identification of the subject (彼) related to the action. "のが" is less common in such sentences but not grammatically incorrect. It just changes the emphasis slightly.