The word is derived from the Greek "κεφαλή" (kephalé), meaning head, to which are added: "εν-" (en), meaning inside and "-ιτις" (-itis), meaning inflammation. The word in English has come via Latin, then French.
The C in romance languages is "soft" before E, I, and Y (e.g. receive, decide, cede, city, cyanide, cynical) and "hard" before A, O and U (e.g. cat, cot, cut). Exceptions in French are indicated by the use of the "softening" cedilla: "Français", "Çendrillon". Céphalique in French has no cedilla and should be pronounced "hard": Ke-fa-LICK.
In English the classical pronunciation is en-ke-fa-LIGHT-iss. This is consistent with etymology and the French cognate word.
All words derived from Greek "Kephalé" are pronounced in a similar way with the "hard" C: Encephalogram, cephalic, cephalopod, encephalin, etc, etc.
Similarly, the word Celt is often pronounced with a "soft" C, whereas in Greek "Κέλτοι" (keltoi) and Latin "Celtae" (Keltae) are always pronounced with a "hard" C.
As far as the pronunciation of "apoptosis" is concerned, as it is also derived from the Greek, the two "P's" should be pronounced, as they are in the original language: A-pop-TOE-sis.
