The upstream default for pacman.conf will be acceptable to overwrite in this case, though the fact it created a pacnew tells me you added some repo or otherwise augmented that file, or else the pacnew would not have been created, and by overwriting it you will lose this additional configuration you made.
This will not break your system, but may have been unexpected.
(ex: if you added chaotic-aur
before … thats why the pacnew … and now it will not be there)
If you repeat this process on other files … such as /etc/shadow
… then you will be met with a broken system.
I will repeat: