One ship at a time, might be accomplished by using the spawn ability of the fleetbeacon, which is predominantly used by the vasari, however i have seen some mods give this to the other races as well.
But if you spawn a ship this way, you can determine its lifespan, i believe, same as spawning from combatturret, though combatturret spawns only frigates (you can build "like" capitals here (frigate equivalents, but without leveling) and other frigates of course)
say a lifespan of 900 seconds = 15 min. Have the respawn time, at whatever cost you want and set the re-spawn time to something after the 900 second life of the ship that was made.
It has been sometime since i looked at the fleetbeacon, so i may be mistaken on the ability to limit lifespan. You could consequently make the hull/shields a particular value if you expect the ship to only survive a particular time. Say at half normal value, those ships may only last one or two encouters (even with Pirates, especially in Diplomacy where they are so powerful!). And have the re-spawn time out enough that there would not being any overlap with a ship that has already been created.
The destruction of a "special" building or craft to create the ship is interesting, and i see no reason why it wouldn't work, except how do you control the re-creation of the buildings?
hmmm....
Interesting problem.
Would be fun to look into it though, 
Let me know if you get anything workable.
I can look as well and let you know if i find something that is worth trying.
Take care,

-Teal
p.s Tymestar.... nice idea!!