Lopez would be court-martialed for the loss of her ship, and in the context of the modern GTVA military, she almost certainly would be found guilty and punished severely. While initiative and independence are valuable and even desirable traits in any commander, the post-Capella GTVA is all about exigency, the ability and willingness to make extremely tough Sophie's Choice decisions without hesitation or half measures. Lopez would be held to that standard.
Moreover, disobeying a direct order from a superior officer is an act that can usually only be justified when the order is immoral. While I suppose Lopez could make a case here, in the climate of the contemporary GTVA military, she'd lose.