Playing the Vasari on Single Player FFA on Systems Of War (which is a 5-star, 50-planet map), I eventually got to the point of having all researches and a maximum fleet. The rest of the game involved me hunting down the remaining empires on the other star systems. The Returning Armada skill began to hurt me in this regard. The Dark Armada would spawn at over a dozen planets where I had built the Phase Stabilizers for quick phase jumping. This put my fleet capactity in the negative hundreds,
A kryo noted, this shouldn't be possible - Returning Armada should only summon ships when you have positive capacity, so it should only be able to go one ship's worth of negative (for example, your remaining capacity is 1, Returning Armada summons a ship with a capacity cost of 6, the ship arrives, your capacity becomes -5 and new ships stop arriving).
Do you have a replay of the game you could post?
even though I had full fleet capacity research and there was no way of getting it back to a positive value, except scouring down all the planets with Phase Stabilizers, scuttling the Dark Armada units,
As others have mentioned, simply turn off the autocast on your Phase Stabilisers if you want them to stop summoning ships.
and hoping I could rebuild my actual fleet before another Dark Armada spawned.
Erm, I use the Dark Armada ships to build my fleets...
The Dark Armada are nice as a supplementary defense for your planets, but they become pointless as they use up your supply.
Ah, yes, if you're using them as defences, I can see the problem. I use them as factories that produce ships for free.

And since the Returning Armada skill is at the final technology level, by the time it is researched there isn't a need for it.
It's possible to tech up to Returning Armada within an hour of starting a (normal speed, normal research) game - in fact, teching directly to it is a valid strategy for the Vasari, at least in single player against Hard AIs.
I suppose I could scuttle Military Laboratories until the last level of military research is unavailable to effectively stop the research.
Returning Armada is a civilian tech, not a military one.
I do not know if there is a way to undo research
I've not had it happen to me, but as I understand it, if you don't have enough labs for a tech, it stops functioning - or at least you can't build new ships based on the tech.
but in future games as the Vasari, I will never research Returning Armada.
Entirely up to you, of course, but I fear you're denying yourself one of the Vasari's greatest strengths. It would be like playing TEC and not researching trade centres...