Hmm, I hadn't actually thought of that. There could be one of several solutions to that issue:
1. Only the troops belonging to the owner of the staging area take up farm space and if a player wishes to support and defend their staging area from attacks they must withdraw troops currently stationed their in order to free up farm spaces. Other players would be able to support the staging area as normal, with the troops not taking farm space and not being able to move troops from the staging area elsewhere before they return to their home city.
2. Use two different troop movement mechanisms. One is for transferring troops to a staging area that the player wishes to use in further movements from the staging area and the other is the standard support function from which the player will be unable to move troops until they return to their home city.
3. Stick to the idea that only the player who owns the staging area can position troops in it. Therefore allies cannot aid in the defence of a beseiged staging area. This would make the staging area even more of an offensively orientated asset.
That was a little bit tough to word, if you have any confusions then just post and I'll try to word it better
Another idea that also just struck me is what happens to troops that are positioned in other cities or out on attacks that were sent from the staging area when a staging area is destroyed by a conquest from another player. I would like to offer two suggestions:
Either, the control of these troops will immediately return to their home cities so support can be recalled and completed attacks will return to the home cities.
Or, these troops simply die off, similarly to how troops will die off if their parent city is conquered.
I will edit the original post depending upon the feedback