I think that is very likely to be possible in the more final versions of the game.
Right now all AI Battles just use the instant-autoresolve, but in the future it's likely that they'll just take place normally and take up some time instead of being instant.
Battles between AI Armies in the Mount&Blade series behave like that and you can join any ongoing battle, also AI armies can join each others (or your) battles to help either side.
Since it is not only interesting gameplay-wise but also helps with immersion and, more importantly, balance* it is very likely to be implemented at some point.
*
The autoresolve right now puts more weight into an abstract value for "power" than it does into correct ship choice and setup.
Taking a modded game as an example: A single Alien Behemoth ship (huge powerful ship) will very often win autoresolve battles, but if you fight against it manually it is very easy to defeat it (due to how poorly it's standard setup is and how the AI cannot handle it's flux correctly) even with very weak fleets that would lose every autoresolve fight against it.I suspect the battles are coded for 2 and only 2 sides.
Fleets joining a battle would simply be given the option to join either of the sides, but only if that faction is at least neutral with them. And joining a battle between two hostile forces would simply not be possible.
And I doubt making the ships from the allied fleet not controllable by the player is that far away from the current implementation.