You can do lots of things, e.g. stage an online protest, sign petitions, vote for different parties in the next elections (and it's not as if you don't have a choice; compared to the US with its two-party system, you can really pick your favourites in Germany), call your representatives, join a political party or create a new one, sue the government, ...
What you can't do is unilaterally decide that you don't like a law and ignore it. Asking other people to gather outside for a demonstration when this kind of action is currently disallowed is incitement and therefore illegal.
As others have said, debates around the current measures are allowed and happening. Several parties have already filed lawsuits. In all cases that I know of, the constitutional court has rejected the preliminary injunctions. This means that, while the constitutional court may still decide in the future that the laws were anti-constitutional, they have decided that the harm to the individual due to these laws does not outweigh the harm of these laws not being enforced _were_ they constitutional.
As to whether they needed to shut down the web site or whether that is actually legal: I don't know. But the police, especially local police, sometimes does things of questionable legality, as in every country. Of course, you can always sue the police and demand that your website be restored, and then the courts will examine your arguments. It's not a perfect system (no system is), but you do have legal options.