Unfortunately, neither Dragon nor Marine is strong enough to quell the civil war that errupts, and, as in real life, the outcome may not be all that was hoped for.
You could just leave things like that, but Indy's games are complex and sophisticated, so you may prefer to try for another ending. If you read carefully you will see that it was Marine's team's win that caused all the problems. With a bit of thinking you could figure out that there might be another ending if Marine's team didn't win, but that leaves lots of possibilities. Try some different things and you'll get several different endings. What happens if Marine's team gets so discouraged that they don't really give their best and Dragon's team wins more than half right away? (I didn't try this scenario yet, but I bet there is an ending because I remember that Dragon told Salome that he would begin to think about the problems faced by the citizens in the outlying areas!) What happens if Dragon's team wins, but the results are really close? (The Wise Sage will let you know what happens if you let this happen.)
Spoiler: show
Instead of being discouraged because there are many endings, be happy that you actually got more playing time for your money! Besides, the dialogue during the fights changes, so you get extra there as well!