Based on the possibility of a transition to strange quark matter inside neutron stars, we show that the influence of the magnetic field expected to be present in neutron star interiors has a dramatic effect on the propagation of a laminar deflagration, generating a strong acceleration of the flame in the polar direction. This results in a strong asymmetry in the geometry of the just formed core of hot strange quark matter which will resemble a cylinder orientated in the direction of the magnetic poles of the neutron star. We show here that this geometrical asymmetry gives rise to a bipolar emission of the thermal neutrino-antineutrino pairs produced in the process of strange quark matter formation. These neutrino-antineutrino pairs annihilate into electron-positron pairs just above the polar caps of the neutron star giving rise to a relativistic fireball, thus providing a suitable form of energy transport and conversion to gamma-emission that can explain short gamma ray bursts.