A holographic description of BCS superconductivity is given in arxiv:1104.2843. This model was constructed by insertion of a pair of D8-branes on a D4-background. The spectrum of intersecting D8-branes has tachyonic modes indicating an instability which is identified with the BCS instability in superconductors. Our aim is to study the stability of the intersecting branes under finite temperature effects. Many of the technical aspects of this problem are captured by a simpler problem of two intersecting D1-branes on flat background. In the simplified set-up we compute the one-loop finite temperature corrections to the tree-level tachyon mass using the frame-work of SU(2) Yang-Mills theory in (1 + 1)-dimensions. We show that the one-loop two-point functions are ultraviolet finite due to cancellation of ultraviolet divergence between the amplitudes containing bosons and fermions in the loop. The amplitudes are found to be infrared divergent due to the presence of massless fields in the loops. We compute the finite temperature mass correction to all the massless fields and use these temperature dependent masses to compute the tachyonic mass correction. We show numerically the existence of a transition temperature at which the effective mass of the tree-level tachyons becomes zero, thereby stabilizing the brane configuration.