It's certainly true that you can't shoot a whole film in a "Covid-secure" environment. However, for most of the films in production now, they have already shot large parts of the movie, and so can use this time to do some smaller scale scenes. Or the films that are just starting to shoot, they can do the "covid-safe" scenes now, and then do the scenes which require more people together at another time. Films have reshoots all the time and given how long a film's production takes, I'm sure it will be feasible to complete the movie the way they wanted.
Also just as a general point. Scripts get re-written all the time. For all sorts of reasons - practical/financial etc.
You can make a movie within lots of parameters, and good filmmakers can still make good films out of that.