The point is, it's not that the EU governments are cracking down on anti-semetic views that's worrying (anti-semetism = not good), but more that a precedent has been set where the disputing of officially true information can become a crime.
Here's an extreme example:
You are a member of an oppressed minority.
One day, the government sends troops into your city and 50,000 other members of your group are killed.
The government says that only 100 were killed, by "vigilantes."
You publicly dispute this.
The government puts you in prison.