Update:
Capturing the enemies' capitol does indeed destroy the space ship, even once it is transit. Unfortunatley, this is a very temporary solution- the next turn those evil Russians had already built a handful of pieces for their next ship. Furthermore, they returned the favor by nuking and capturing my capitol, destroying my own space ship in the process.
This resulted in a very ugly WWIII. Any hope of a peaceful resolution was gone.
A few more questions:
1) Is it possible to destroy the second space ship?
2) How?
I ended up destroying the entire Russian civilization, but I never saw a second "Russian space program cancelled" message. I had no chance to rebuild my own ship because I was busy fighting WWIII.
In case anyone cares, here are some screen shots:
As you can see, I lost 1,970 points because the nukes created so much pollution.
More questions:
3) I earned a 1,044 "bonus score". Why? Is this my bonus for conquering everyone else?
4) It says I am "Emperor" of America, but I was in "King" mode. Is this a glitch? Is my version of civ1 corrupt? (Mac OS X running DOSBox).
5) After going "nuke crazy" I began to see red citizens in my cities, next to the "regular" unhappy citizens. What's the deal? Are they super-unhappy? Have they become radioactive?
And, in case anyone else is reading this, here are a few observations I have made:
1) Kill the mongols. A.S.A.P. If you let them survive into the modern age they will spread like a virus and mount increasingly aggresive sneak attacks. Luckily their tech sucked (if they had nukes I might have lost).
2) Using nukes and infantry, you can capture an entire enemy civilization in a few decades. However, this causes many problems. The pollution wrecks your score. The citizenry take to the streets in protest. My democracy collapsed into a far less lucrative monarchy, after which it was impossible to afford the upkeep on most of my city improvements. This resulted in two dozen "The mayor has fled" messages before each turn (very frusterating

).
3) It is possible to clean up pollution using settlers (hit "p" once on top of it) but it takes a few turns to complete the process, and in a warzone you will almost certainly lose the settlers to enemy fire before they finish cleaning.
4) Civ1 rules, and is highly addictive. I haven't gotten a full nights sleep since downloading this damn game. Beware! BEWARE!
Emperor mode, here I come!