"He thinks that ideology is good so for him the glasses are ideology, not the cut-through-ideology tool."But he's deluded. Regardless of his beliefs, the aliens have in fact imposed an illusion (or "ideology" in Zizek jargon) on him, and the glasses do in fact let you see through that (as he himself does later). He can think whatever he wants, but that doesn't change these facts.
"Once you rebel against bullshit your life becomes very uncomfortable real soon."
So, contrary to Zizek's contention, it's not his "enlightenment" that causes problems, but his trying to fight against those with power. A lesser man might have thrown away the glasses after seeing the truth, or perhaps consciously and deliberately started cooperating with the aliens, as various traitor characters did in The Matrix and V, for example.