Clearly there's a bit of code in there now that says "when characters beam to a new place draw their weapon". It ought to be easy enough for the Devs to eventually code up an option that allows you to decide whether characters will automatically draw their weapons when beaming or not.
Remember that characters will automatically draw their weapons if you attack a target with holstered weapons so the there's really no real risk to you if you choose to keep your weapons holstered while beaming. Theoretically most people are not going to agree to beam down to a place where they need to fire weapons instantly anyway even in wartime.
I'd like it if it auto-holstered my weapon when beaming onto social maps (e.g., Stardock, my own ship's bridge, etc.), or when doing non-combat missions (e.g., talking to miners, scanning 4 pods, etc.). Having weapons drawn when beaming into a potentially hostile situation is fine with me, though.