I think that is not necesary to reform Queen Chrysalis (she is awesome beign evil altough also being "dangerous neutral" could be good) if not to give more deep to her character showing her inner motives for which she does for the swarm. I love to see Queen Chysalis behaving as an honourable queen altough relentless enemy which takes care of the health and happines of her people and taht agree with this someone would not doubt to bring the hell to Equestria if it is necessary to assure the survival of her race.



On other hand, respect Flurry Heart of course she can take her as a hostage but not necessary treat her badly because as being herself the "mother" of her hive (whatever in a figurative or literal sense) knows how harmful is to see suffer your beloved childs and so which would look after Flurry lovingly and even motherly. And who knows? Maybe could form stong bonds between both until the point that in the future she and Flurry can achieve some kind of "statu quo" or"pacific" coexistence (in a symbiotic way) between the changeling swarm and the Crystal Empire.