Edit: Apart from the functions being $L^2$ I am also assuming them to be at least twice differentiable so that I can define the action of $\frac{\mathrm{d}^2}{\mathrm dx^2}$, I am also assuming that the functions have some boundary condition (such as vanishing at infinty) that allows me neglect the boundary terms coming from integration by parts.
Note that the differential operator $\frac{\mathrm d}{\mathrm d x}$ is not hermitian with respect to the inner product (ip2) since integration by parts now gives $\langle f, \frac{\mathrm d}{\mathrm d x} g \rangle = -\langle \frac{\mathrm d}{\mathrm d x} f, g \rangle$. So the operator is in fact anti-hermitian: $\left(\frac{\mathrm d}{\mathrm dx}\right)^\dagger = -\frac{\mathrm d}{\mathrm dx}$.
Your proof of orthogonality of eigenvectors of a hermitian operator holds in general. But whether the eigenvalues will be discrete (quantized) or not depends on the space on which the functions are defined. If the space is compact (such as a circle, or a finite interval (a.k.a. the infinite square well in quantum mechanics)) then the eigenvalues will be discrete, if the space is non-compact (such as $\mathbb R$ from the previous example) the eigenvalues will be continuous unless we impose some extra constraints on the functions to restrict to a space with discrete spectrum (eigenvalues) for the operator. You can only write operators as square matrices and vectors as column matrices if the underlyingoperators have discrete spectrum.
Edit: (Correction, as pointed out by Chappers in the comment) It is possible to have discrete eigenvalues for differential operators on noncompact spaces if the function space is compactrestricted by strong enough boundary conditions (that allows to normalize them for example).
The differential operator in the (assuming time-independent) Schrödinger equation, for a particle moving in a one dimensional space, is: $$ \hat D_\psi := -\frac{\hbar^2}{2m} \frac{\mathrm d^2}{\mathrm d^2 x} + V(x)\,, $$ and the inner product of wave functions is exactly as we defined in (ip2). Therefore, if the potential $V(x)$ is a real function, then the operator $\hat D_\psi$ is hermitian, since we have already proved that the second derivative is hermitian and you can check that multiplication by a real function is hermitian as well. Hermiticity leads to orthogonal eigenvector. But once again, the eigenvalues are discrete if the space in which the paticle moves is compact, or if we impose normalizability which is usually assumed in physical scenarios.
This seems too complicated for me, I'm afraid. The problem is to find a space on which there is some operator that acts on (perhaps a restricted set of) functions defined on that space and the eigenvalues of that operator coincides with the eigenvalues of the matrix. The only thing I can say is that if this can be done then the space will turn out to be compact since the matrix has discrete eigenvalues. Beyond that, I can not say anything useful about how to proceed, sorry!