That definitely sucks - I also hope not too many tourists from far away had looked forward to visiting the zoo (though of course, there's still the Tierpark).
Maybe this is a very stupid question, but is work and research being done to prevent avian flu from having the impact it currently has? In recent years, we've heard billions of news about zoos having to close bird houses and walkthrough aviaries in the cold months, and Berlin's case of closing down the entire zoo is particularly extreme. That won't work in the long term - either zoos have to almost entirely stop keeping birds to avoid all this trouble, or they'll have to find a better way to protect their birds. I've heard of zoos that vaccinated their birds against avian flu in the late summer - couldn't Berlin have done that, or isn't it feasible because they have so many birds compared to the average zoo?