I have two suggestions this time
I'll start with the simpler one, probably:
Would it be possible to use the system we currently use for enemy voodoo, with any ally line of sight that turn up to int counting for the spell, for indirect fire? Bows, mortars, anything with an arc. They know where you are, and if they can do the arc, that should be enough for those. Right? Though probably the computer is still not smart enough to use mortars, does it use crouch at all?
Second idea, which seems far more complicated to me:
Is it possible to set doors that open one way, but not the other, unless specific criteria is met? My idea is to have as vessels giant genetically engineered bugs or something like that, possibly for Deep Ones, or maybe some new xenomorph species. If they're healthy, they'll let you come in, as they wish to eat you, but won't let you out easily; if they're hurt, like if you shoot them down, they don't really have a choice on your use of their 'doors'. Their outer hulls would probably be chitin or something very like chrysalis hide, while inner walls could maybe be rendered into that material Reticulans give, to provide incentive to not just blow the thing up. Inside the creature, it would be dark and have a chem effect that slowly eats away at armor until one side is at 0, at which point it eats away at life. If any of the crew have voodoo, being in front of the creature would count as line of sight. Uh, there could be a heart and brain in the creature, requiring you to kill or maybe capture it to win the map, I honestly don't know how we'd deal with a live ship capture, I imagine the carcass would take up about as much space as the Bonnie hull.
I hope that made at least a little bit of sense, and that it ends up somewhat useful
Oh, and if it was set up Giger-ish, and had squlchy sounds inside, all the better