As I got to the final mission I thought I try an experiment, seeing if it was possible to have a permeant army of aliens at your disposal.
Cydonia is a two parter mission the first is having the team outside in 'space Egypt' with the followup inside the base.
The first mission consists mostly of sectoid commanders and are psionic, so after wrapping up the majority of the aliens I took the commanders while under mind control to the lift that would take to the next stage.
I tried the following.
I Mind controlled the aliens and stunned them, entered the second stage and revive them but they came out hostile.
I then stunned them without mind control and revived them in base and nothing happened.
And if you store them in your inventory they just vanish!
I don't know if the 94 game was patched several times during it's run but unfortunately you can't send out a alien task force under permeant control.
However if you do take the commander aliens, revive them in the latter mission and shoot them I do believe you can affect alien morale in the existing base. Can't say it's entirely proven but I'll test it in the future.