I tried to find an answer that does not (at least in appearance) use eigenvalues. Here it goes.
The following only assumes that every non-negative self-adjoint matrix has a unique non-negative square root which commutes with it.
Let $S$ be the unique non-negative square root of $A^2$. Let $B := \frac{A+S}{2}$ and $C := \frac{S-A}{2}$. The matrices $B$ and $C$ are self-adjoint as linear combinations with real coefficients of self-adjoint matrices.
Then $BC = \frac{1}{4}\left(S^2 - A^2\right) = 0$.
Let us prove that $B$ is non-negative, that is, for every $\phi \in \mathcal{H}$, $\langle \phi, B\phi\rangle \geq 0$.
Notice that $B^2 = \frac{1}{4}(A^2 + 2AS + S^2) = \frac{1}{4}(2AS + 2S^2) = \frac{1}{2}(AS+S^2) = BS$; notice also that and that $B$ commutes with $S$, so that $B^2S$ is a non-negative operator (see for example here).
If $\phi \in \ker B$, then $\langle \phi,B\phi\rangle = 0$. If $\phi \in im(B)$, then there is some $\psi$ such that $\phi = B\psi$, and therefore $\langle \phi,B\phi\rangle = \langle B\psi,B^2\psi\rangle = \langle B\psi,BS\phi\rangle = \langle \psi,B^2S\psi\rangle \geq 0$.
Moreover, it is classical that $\ker B = (im B)^\perp$, so let $\phi$ be any vector; decompose it into $\psi_1 +\psi_2$ such that $\psi_1 \in \ker B$ and $\psi_2 \in im B$.
Then $\langle \phi,B\phi\rangle = \langle \psi_1 + \psi_2, B\psi_1 + B\psi_2\rangle = \langle \phi_1, B \psi_2\rangle + \langle \psi_2,B\psi_2\rangle = \langle \psi_2,B\psi_2\rangle \geq 0$.
The same argument works for $C$.