How does Milton’s Areopagitica represent only a partial advocacy of toleration, constituting failure? How can I discuss this idea?

The approach I would take would be to challenge whether Milton's only partial advocacy of toleration renders the Aeropagitica a failure, and I would argue that in fact a work doesn't have to be perfect to be successful.
One way to start would be to note that politics is the art of the possible. Since Milton wrote the Aeropagitica specifically to advocate for the repeal of the 1643 Licensing Act, which required all works in England to pass by a censor before being published, Milton was appealing to a specific audience with a specific set of concerns. Parliament, controlled by Puritans at that time, was obsessively anti-Catholic and arguably any attempt to roll back censorship would stand no chance of approval without some safeguard against the perceived threat of a Catholic invasion. Therefore, one could argue that Milton had little choice but to add an anti-Catholic clause to his argument if he had any hope of success. Milton was also less than tolerant in arguing that a blasphemous work could be burned or destroyed after it was published. However, he was simply hoping to go back to the system that existed before the passage of the Licensing Act, an easier goal to achieve than abolishing all censorship. Since many people, then and today, would argue that (most notably in politics) half a loaf is better than none, one can make a case that asking for partial relief on censorship was better than no relief at all. To be imperfect is not necessarily to fail.  
Further, while Milton did not at the time persuade Parliament, the fact that the Aeropagitica influenced future legislation undermines the argument that its partial advocacy for tolerance was a failure. For example, the United States Constitution, following Milton's argument, specifically forbids prior restraint, which means it prohibits not allowing a book to be published in order to censor its content. Finally, Milton's argument that truth flourishes best in an atmosphere that allows all ideas to be openly debated has remained influential and, in fact, freedom of the press has become a standard way we evaluate the strength of a democracy.