I like this question, as former SLAC DISer (and TJNAF, MIT-Bates, DESY), where elastic-scattering was used to calibrate the instrument, I've thought about it (long ago).
Also, if you want to tackle quark structure functions, it really helps to compare and contrast with the QM view of the atom. There are similarities (I think of the Lamb Shift as "Sea $\gamma, e+e^-$", for example), and differences (quarks don't have wave functions, yet).
Now I thought the answer was "No", because atoms are neutral. We measure the proton elastic form factor with liquid hydrogen, and then to get neutron data, we use liquid deuterium and subtract. For magnetization, you can use polarized $^3$He, which to a good approximation, is singlet protons and a polarized neutron. When I looked this up, I noticed I was an author on the paper--it was that long ago that I forgot.
So how are you going to deal with a neutral atom?
Your suggesting of subtracting proton scattering is misguided: at atomic energies (say $13.8\,$eV), the proton form factors match the static charge and anomalous magnetic moments--there is no $Q^2$ dependence over the relevant range for atomic physics.
Also, the proton is not stationary in the middle--that is just one of our QM assumptions because we solve the Schrödinger Equation in the reduced mass coordinates (see: my 2nd paragraph--we forget all the things we do to make the Coloumb potential analytically solvable). In the lab, the protons are in there little tiny $Y_l^m$ orbitals with Laguerre radial dependence, too--and the size of the orbital is:
$$a_0 \times \frac{m_e}{m_p} \approx 25\,{\rm fm}\gg r_p \approx 0.8\,{\rm fm} $$
So you're just probing a neutral atom with enough $Q^2$ to resolve a Bohr radius, so:
$$ |Q^2|^{\frac 1 2} \approx \frac{\hbar c}{a_0}
= \frac{197\,{\rm MeV \cdot fm}}{50000\,{\rm fm}} \approx 4\,{\rm keV}
$$
and that is much greater than the ionization energy for hydrogen (it is not a coincidence that it is roughly $2R_{\infty}/\alpha$).
Even before that, there is the experimental difficulty of getting a low enough energy electron beam that can still traverse aluminum windows and vacuum windows into your detector.
But I was wrong. People do it, and it is described here: https://en.wikipedia.org/wiki/Atomic_form_factor .
Here's a nice X-ray scattering result from Chlorine, described in the link:
Of course X-rays don't lose energy through multiple scattering, so that helps experimentally.