I'm a newbie here, but as with HeroQuest, it seems you can pretty much do whatever you think is best. I don't own the Dreadnought expansion but as with HQ they don't assume you have all expansions, so combining them is probably going to be a "best guess" of the GM (Alien/Chaos player). That said...
Since the Eldar models don't fit the gun turrets, you could either compensate them by giving them the bonus "heavy" eldar like you said, or just give them the spare Marine with the turret and treat them like a regular Eldar soldier for purposes of any bonuses from cards in that faction (and then just add another regular Eldar with a heavy weapon IF the spare extra Marine would have gotten a heavy weapon). The latter option would seem more "fair."
I look at the Eldar faction as being equivalent to a Marine squad, because although the Exarch has only 1 life point, he has his skill/power cards that can absorb damage making him equivalent to a Space Marine Commander. The extra troops (Eldar soldiers #6-10) are normally only used when their full faction is taking the place of two Space Marine Squads (which in my view doesn't quite work, because you'd be replacing TWO Commanders and a single marine is not equivalent to a commander!).
With the Orks I would take the same approach for the same reasons above. Not giving these factions a Tarantula trooper (+ regular trooper) would weaken that faction and increase the difficulty. If adding them to the three marine factions (and each having the turret + 2 extra marines), the Chaos player is really going to be overwhelmed, because presumably the Dreadnought expansion is enhancing the three existing marine factions from the core game.
To make things seem like it fits, you could just not "attach" the miniature to the cannon and use the appropriate figure to take the place of the "super heavy weapons" space marine meant to operate the cannon, turret or whatever you want to call the Tarantula. I would think you'd want to use the scout as a scout rather than just an operator, but if that's all you had, why not?
I forget if it's possible to destroy the enemy's turret and leave the soldier alive, because if so, then using a non-Marine character would matter in terms of offering that uniqueness for the unit. So your choice...
