I'd go to war. I realize our country and freedoms need to be protected, and even if I did or did not agree with the reasoning behind any given war, I'd still choose war since I want to be one of the many protecting our freedoms. Some countries wouldn't give you a choice of war vs. jail - they'd just put a gun in your hand and send you to war.
Not only that, but once I return home, I am considered a hero (though this would not be the reasoning behind choosing war over jail) and can proudly dispaly my veteran status on resumes, etc. An ex-con? They are denied jobs for haven been in prison, they are looked down upon as deadbeats of society. No thanks - I'll be the hero who upholds our freedoms and protects those freedoms.
Now that said, would I join the military tomorrow to go to war? Not on your life! :p I am too much a wimp - I mourn over a squashed bug. I could never witness death, and could never inflict death myself. But given those two choices, I choose war.