If this were Polish it would be in the instrumental. Otherwise it's nominative because "esse/to be" is a verb of state that compares or equates. There is no action going on. As Danielconcasco said here four days ago:
We don't use accusatives with esse (to be). There is no direct object, receiving the action.
Livia doesn't act upon the student, she is the student.
I'm having a problem with what has to be a very basic point. A dictionary says "discipulus" is a 2nd declension noun and its gender is masculine. I realize after reading this discussion, the form in the sentence is nominative. When I look at a chart of declensions there is only a choice of singular or plural with no mention of gender. I get a little obsessed with things like this (things I don't understand) which interferes with my ongoing learning. Thanks for your help in advance.
We'd have to know which dictionary you're using to know for sure, but in my experience it seems pretty common for a noun entry to simply that word's gender give its declensions even when there is a variant in either or both of the other genders.
It's adjectives that tend to list masculine, feminine, and neuter declensions together, since they have to match arbitrary nouns.
Discipula is its own word. Or atleast you can consider it that way. They are listed seperately. Just like many languages have different words for the male and female versions of an occupation, english only has a few it took me forever to think of one! Actor and actress.
Btw wiktionary is kind enough to show the female/male variant in its entry. (Not the chart, just a clickable mention)