I am okay with the fact that we can find a pair of orthonormal eigenvectors, but how do we know that we can find some of the form $q_1=(x_1,-y_1)^T$, and $q_2=(y_1,x_1)^T$?
NOTE: I'm not sure if we need $A$ to be real matrix here, but if so feel free to assume it.
Edit:In response to being possible duplicate... that question is about diagonalization and why eigenvectors of a real symmetric matrix are orthogonal. my question here is about why there are orthogonal eigenvectors of a certain form.
That is, we know that there are orthogonal eigenvectors. But how come the orthogonal vectors $q_1=(x_1,-y_1)^T$, and $q_2=(y_1,x_1)^T$ are eigenvectors (as opposed to just being orthogonal vectors)?
Pick any eigenvector $\mathbf v=(y_1,x_1)$ of $A$. What do the vectors $(x,y)$ that are orthogonal to it look like? Well, we must have $(y_1,x_1)\cdot(x,y)=y_1x+x_1y=0$. This is the equation of a line through the origin with direction vector $(x_1,-y_1)$, i.e., every vector orthogonal to $\mathbf v$ is a scalar multiple of $(x_1,-y_1)$. You agree that $A$ has orthogonal eigenvectors, which means that $(x_1,-y_1)$ in particular is itself an eigenvector of $A$. If in addition $\mathbf v$ is a unit vector (which we can always arrange by normalizing any eigenvector of $A$), then it should be clear that $(x_1,-y_1)$ is also a unit vector.