First things first
At $T=0$, the ion cores (i.e. the nucleus of the atom + electrons in lower shells) form a perfect lattice (assuming no impurities). As Bloch Theorem shows, electrons (or better: Bloch waves) do not scatter in a perfect lattice. So even though both the electron and the ion cores have non-zero net charge, they do not interact. This is very important!
How atoms can vibrate
This is a bit of a weird question for me. I know quantum mechanics is strange and can be unintuitive, but don't toss your intuition out of the window. Think back to how one goes about solving the Schrödinger equation for a single atom. The first approximation one makes is the Born-Oppenheimer approximation. It uses the fact that the nucleus is much heavier than the electron shell. So in most cases, one can think of the position of the atom as a whole in a classical picture: vibration or oscillation of an atom is described by $\langle\mathbf{R}\rangle = A\cos\omega t$, where $\mathbf{R}$ is the position operator of the center of mass of the atom.
Phonons (classical and quantum mechanics)
To be precise, the word phonons as a quasi-particle only makes sense within quantum mechanics. But, in order to get there, let's start with a classical treatment. The ion cores arange into a lattice, because there is repulsive interaction between them (they have the same charge). In the simplest case, the repulsive energy is minimized when they align in a perfect cubic lattice (also called simple cubic, sc). To lowest order, the potential a single ion core feels is harmonic. When it is brought out of equilibrium, it oscillates around that potential minimum; a classical simple pendulum. In a lattice, this movement also excites the other ion cores to oscillate. Due to periodic boundary conditions, only a discrete set of motional frequencies is allowed. As we always do, we want to find the eigenmodes and eigenenergies of the system (still classical treatement here!). This is were optical and acoustic phonons come from. In this classical picture, the word phonon refers to these eigenmodes of oscillation. To turn this into quantum mechanics, we can treat the displacement of the ionic cores as a field and quantize it canonically. The eigenmodes are delocalized over the whole crystal. The way to think about electron-phonon interaction is to imagine a localized electron and phonon (superposition of many Bloch waves and phonons). One can picture this localized phonon as a positive charge cloud the negatively charged electron interacts with. Now we have turned electron-phonon interaction into a scattering problem of a negative and positive charged particle.
The important thing to take home is that electrons DO NOT INTERACT WITH THE LATTICE (edit: more precise is "they do not scatter from the lattice). You can't think of it as scattering of an electron with a single atom. You have to think in this delocalized phonon picture, which disrupt the perfect lattice structure and serve as scattering sources. Electrons only interact with lattice imperfections They allow the excited electron to relax into a lower energy state. If there were no phonons (i.e. $T=0$) or lattice defects, the electron could only relax by emission of a photon (or electron-electron scattering, but that still leaves you with an electron in an excited state).