Did the following incident/statement from the 2007 movie Persepolis really happen?

Unfortunately the major inaccuracy one could interpret from the film's quote is that male prisoners were automatically exempt from sexual abuse, as this report from the Iran Human Rights Documentation Center shows:

Surviving Rape in Iran's Prisons

This report documents the ordeals of five former prisoners – two women and three men – who provide their first-hand accounts of being raped, witnessing rape or being threatened with rape during their detention in Iranian prisons.

Interviews with additional victims go into further detail about other sexual abuses witnessed while they were prisoners (1982-1990):

One of the most common finds is that female political prisoners, especially during the years when we were in prison, were mostly 17 or 18 years old—young and unmarried. [The torturers, guards, authorities] thought that girls must be raped before being executed so that they don’t go to paradise. This was systematic. They had religious justification behind [such belief].

• Female Prisoners Raped Before Execution “Lest They Go To Paradise” (iranbriefing.net)

Lahidji, who has been monitoring human rights in Iran for three decades, says that over the years he's received a number reports about political prisoners being raped by their interrogators.

"Unfortunately, in the 1980s we used to receive a lot of news about girls being raped in prison before being executed,"

• New Prison-Rape Allegations In Iran Bring Practice To Light (RadioFreeEurope/RadioLiberty)

Published reports are available about these types of torture committed against women political prisoners after the 1979 Revolution. The most systematic type of reported rape has been the rape of virgin girls who were sentenced to death by execution because of political reasons. They were raped on the night before execution. These reports have been substantiated by frequent statements from the relatives of women political prisoners. On the day after the execution, authorities returned their daughter’s dead body to them along with a sum considered to be the alimony. Reports state that in order to lose their virginity, girls were forced to enter into a temporary marriage with men who were in charge of their prison. Otherwise it was feared that the executed prisoner would go to heaven because she was a virgin!

• Feminist Attorney Speaks Out Against Rape As a Weapon of Torture in Iran
  (iranianvoicesintranslation.blogspot.com - translation)
  (original source "Rape as Systematic Torture in Iran" meydaan.com)

It's always dubious to count on movie accuracy, and you have to ask yourself, how would our heroine (who is, what? 10-12 years old?) know about such things occurring? It's obviously not something that she could personally witness, and obviously not something where there'd be, y'know, someone to say, "Yes, this happened to me!"

Furthermore, the point of a Reign of Terror is, of course, the terror, and it might just be that this is the sort of rumor you'd want floating around. "Do what we say, or this will be your fate," whether or not it actually would be or not.

That said, there are plenty of documented atrocities of that time period, and more and more seem to be emerging in the past 15 years or so. I would not be particularly surprised if it were true, but this is not proof.

There's a long discussion and debate on Reddit on this topic which you might wish to read.