Possible 4.4 spoilers:
The end of the 4.4 MSQ did show Alphy and Shadowhunter discovering that someone is using Black Rose, which I definitely think could be used against Ala Mhigo as what could be the first large-scale test of its effects. That said, it's possible that Alphinaud could somehow get word of plans to use it in Ala Mhigo, find a way to relay a warning to the Alliance, and prevent it from causing too many casualties. Even so, I would expect that once Black Rose has done its work and cleared up, the Garleans would probably follow up with a direct assault to raze the city and finish things off with the least amount of resistance. It would be a huge loss to the Alliance after all the efforts to liberate Ala Mhigo, and could show exactly what we'll be facing going into the next expansion. Of course, I expect there's every possibility things could end up happening way differently, but it is a scenario I can see happening in any case.