My impression is that the writers, director, and producers of the movie wanted to make the story a bit more topical and timely. I also suspect that they were worried about how strange and even silly the sudden appearance of a gigantic, psychic squid would seem to the audience.
Therefore, they decided to insert a connection between Adrian's evil plan on the one hand, and the climate change crisis on the other hand. There was no need, or even desire, for a monster squid to show up at the end of the film. The climax, now that the squid was no longer needed, involved two conflicting entities: Adrian and Dr. Manhattan.
Instead of addressing the Cold War exclusively, the movie could now also make reference to climate change, renewable energy, and the environment. This was desirable, because when the original comic books were written, the Cold War was still going on, but when the movie was made, it had been over for more than 20 years.
All of these factors combined to produce the ending we saw on the screen: a weird psychic squid was replaced by a more sensible and, in a way, more plausible, attack with much more familiar weapons, which allowed the audience to maintain their willful suspension of disbelief - something that would have been far less likely if they saw an enormous cephalopod destroying New York for no apparent reason.
In a comic book, a huge squid killing millions of people is pretty much par for the course. In a modern movie, on the other hand, it is likely to raise a few eyebrows, and attract quite a bit of criticism from people who have never read the comics. It just seems weird.