I seriously doubt LucasArts was trying to make a statement about war in general. It's much more likely that since Anakin did it in the movie that they felt the need to include it in the game. But as RRS-1980 said, since you're playing the good guys, the women and children shouldn't be there or you should be able to avoid them.
The last Star Wars RTS I played had you playing on the side of the Empire when you killed Ewoks during an initial scouting mission to Endor. Even that game showed the character having remorse for killing animals that were only protecting their territory. The same character later defects and joins the Rebellion.
If you really want to teach people about the results of war, have them play a game like Brothers in Arms on Realistic mode. No saving during missions. You die, you start over (which isn't realistic, but it keeps you from picking up where you left off). Or even better, play something like America's Army. You die, you do not respawn. You wait until the round ends because YOU'RE DEAD. In other words, if you really want to teach people about the realities of war, pick a game that isn't based in a fantasy universe. Star Wars is suppose to be fun and having a Star Wars game where the good guy is pretty much required to kill children is really lame.
Hell an even better way to teach people about the results of war is to actually teach them about real wars. Show them photos of what has happened in the past. Kids need to be old enough to understand everything involved though, otherwise you're just going to scare the crap out of them with gross pictures.