Is it possible to stop enemy spaceship form reaching it s destiny after it has been lunched without annihilating whole civilization?

IIRC, raze their capital city and it'll cancel their mission.

is there any other way

No

:viking:

Welcome to the Forums abraksil. :beer:

Once they launch, you have two choices.

1) Destroy their capital.
2) Launch your own ship with all components - hopefully it'll be faster.