Rather than handing over the clone to Kanta or making a massive raid, have a (huge?) story point use to make a sneaky break out of Zal, or perhaps convince Kanta with your bravado (sounds pretty unrealistic) to sell her. (I like being an 'ethical', no crew lost type of captain
, and giving up either marines or a clone to be tortured is hard).
Maybe the player can be rewarded in little things for huge story point spends, like allowing the clone to be a level 1 officer if you don't hand him over? Warlord Locke had some operational talent, his clone could have inherited that.
Another example I saw someone mention is, if you have a hegemony commission you shouldn't have to sneak in to hack the relay, perhaps by using story points, a commission or good relations you could request to access the relay or even the archive directly (surely a small unimportant archive such as this wouldn't be classified as SUPER ALABASTER). So the provost could give you an option to either hack it, get hired by the hegemony or build enough relations and favour to access it directly.