Indeed $P(\mathbb{N})$ is not free. All infinite freely generated Boolean algebras are atomless, while $A$ is atomic. Furthermore, only the Boolean algebras that are generated by a finite set $G$ are finite (with $2^{2^{|G|}}$ many elements -if I'm not mistaken).
To see that if $G$ is infinite then $A$ is, is trivial. To see that if $G$ is finite then $A$ is finite you just need to check that $A$ is the Lindenbaum algebra of propositional logic with $|G|$ many atoms (check that this algebra satisfies the requirements).
To see that if $G$ is infinite then $A$ is atomless you do the following: Take an atomless Boolean algebra $B$ with $|G|$ many elements and define a mapping $f:G\to B$ such that $f[G]$ is dense, i.e. for every element $b\in B$ there is some element in $c\in f[G]$ such that $c\leq b$. Then take the homomorphism $\bar{f}$ that extends $f$. If $A$ has an atom $a$, take $f(a)$, since $B$ is atomless, there is some $d and there is some $c\in G$ such that $f(c)\leq d$. Then $0 while $f(a\land c)$ is either $0$ or $f(a)$.
Actually you can completely describe what the freely generated Boolean algebra looks like, though it's a bit troublesome. You can find this is, for example, in Jonhstone's "Stone Spaces" (at the very end of the first chapter). The basic idea behind the construction lies in the fact that all propositions can be written in disjunctive normal form.
P.S.: I don't think your argument is correct, because you didn't seem to use the infiniteness of $\omega$ and as I have argued there are atomic freely generated Boolean algebras.
EDIT: The problem with your argument is that you assume that $\bar{f}$ will be an automorphism but this may not be the case. All that is required is that $\bar{f}$ is a homomorphism, which doesn't need to preserve atoms.