Until Berta and Ernst Scharrer established the concept of neurosecretion in 1928, scientists believed that either cells secreted hormones, which made them endocrine cells and thus part of the endocrine system, or conducted electrical impulses, in which case they were nerve cells and thus part of the nervous system.
a) either cells secreted hormones, which made them
The idiom is either A or B, A and B should be structurally parallel. Here "cells secreted hormones", a clause, and "conducted electrical impulses", a verb phrase, are not parallel. So to make them parallel cells should be placed before either. Also pronoun them has no clear referrent.
b) either cells secreted hormones, making them
either...or.... structure violation.
c) either cells secreted hormones and were
either... or violations. Also "and were" changes the meaning and also grammatically wrong in this sentence.
d) cells either secreted hormones, in which case they were
Correct. either...or.... structure is fine. Also in which they were is parallel to the structure in the later part of the sentence.
e) cells either secreted hormones, which made them
either ...or.... structure is fine. "which made them" is not parallel to "in which case they were..." and also changes the meaning. hormones doesn't made them endocrine cells, but they are identified as endocrine cells.