Hybrid superconductor/magnetic tunnel junctions of Nb/CoFe/AlO/CoFe/NiFe have been implemented to investigate the impact of the superconducting Nb layer on the proximal ferromagnetic CoFe layer. A suppression of tunneling magnetoresistance effect is observed as the Nb layer undergoes the superconducting transition. This suppression is thought to be due primarily to the coupling of the magnetic inhomogeneity of CoFe to the superconductivity of Nb. The magnetic structure-vortex interactions interplay each other, inducing a complex domain evolution in the magnetization process and consequently degrading the junction's antiparallel magnetization alignment.