Using femtosecond time-resolved x-ray diffraction we investigate the structural dynamics of the coherently excited A(1g) phonon mode in the Fe-pnictide parent compound BaFe(2)As(2). The fluence dependent intensity oscillations of two specific Bragg reflections with distinctly different sensitivity to the pnictogen height in the compound allow us to quantify the coherent modifications of the Fe-As tetrahedra, indicating a transient increase of the Fe magnetic moments. By a comparison with time-resolved photoemission data, we derive the electron-phonon deformation potential for this particular mode. The value of Δμ/Δz=-(1.0-1.5) eV/Å is comparable with theoretical predictions and demonstrates the importance of this degree of freedom for the electron-phonon coupling in the Fe pnictides.