She was a part of the group of students that barricaded themselves inside Hopes Peak during the 4th year. This is supported by the fact that when Makoto watches the student interviews (declaring that they stay in Hopes Peak forever) the video mysteriously cuts out before Junko is shown.
That's the thing though: why did they barricade themselves in Hope's Peak? To avoid the Ultimate Despair, which = Junko. They wouldn't be closing themselves in the building with Junko, even if she was a fellow student, knowing that she was the cause behind it all.
Actually, the cast probably didn't know. Izuru was probably the face of the tragedy to the public until the events of DR1. Anyone that knew of Junko's involvement had already been killed by the time the school shut down.
I think some of this is implied in DR0.
If she was in the shadows manipulating everything, it makes much more sense, sure. It's kind of hard to think she'd convince thousands of students to kill themselves for her and a bunch of other crazy stuff without it being openly known, but alright.