Using the similarity matrix $X=\begin{pmatrix}1&0&0\\0&9&0\\0&0&3\end{pmatrix}$, $A$ is similar to the circulant matrix $A'=\begin{pmatrix}0&0&9\\9&0&0\\0&9&0\end{pmatrix}$. This $A'$ has an easily found square root $B'=\begin{pmatrix}0&3&0\\0&0&3\\3&0&0\end{pmatrix}$. Now, reverse the similarity, and
$B=\begin{pmatrix}0&\frac13&0\\0&0&9\\9&0&0\end{pmatrix}$ is a square root of $A$.
So there's a rational square root - but that's not an integer matrix. We need to look deeper. $A'$ can be diagonalized by the Fourier matrix; its eigenvalues are $9w^2$ for each cube root $\omega$ of unity, with eigenvectors $\begin{pmatrix}1&\omega&\omega^2\end{pmatrix}^T$. With this complete set of eigenvectors with different eigenvalues, any square root $B'$ of $A'$ must share those same eigenvectors, and its eigenvalues must be square roots $\pm 3\omega$ of the corresponding eigenvalues of $A'$. That gives us eight possibilities.
First, if we take $+$ signs everywhere or $-$ signs everywhere, we get $\begin{pmatrix}0&3&0\\0&0&3\\3&0&0\end{pmatrix}$ or $\begin{pmatrix}0&-3&0\\0&0&-3\\-3&0&0\end{pmatrix}$. Undoing the similarity, these each lead to square roots of $A$ with one non-integer entry as found before.
Taking a $-$ sign for the eigenvalue $1$ and $+$ signs for the other two eigenvalues leads to $\begin{pmatrix}-2&1&-2\\-2&-2&1\\1&-2&-2\end{pmatrix}$. Reverse the similarity and we get a square root $B=\begin{pmatrix}-2&\frac19&-\frac23\\-18&-2&3\\3&-\frac23&-2\end{pmatrix}$. Of course, taking a $+$ sign at $1$ and a $-$ sign at the other two would lead to the negative of this matrix. (See also @user's comments on the question)
The other four choices come from taking different signs for the two non-real roots. The trace of the square roots we get out of these have nonzero imaginary part $\pm 3\sqrt{3}$, so they can't be rational.
So then, $A$ has four rational square roots. None of them have integer entries, and thus the answer is no.
Your argument, on the other hand, fails; it's an attempt to prove that there aren't any rational square roots, when in fact there are.