Firstly,
Welcome to the forum
Secondly, get Resistance/GOTY if you possibly can. It's very well worth it. You can buy it for $10 now although you may have to hunt around a little.
Thirdly, your questions.
1. They are fleeing because they are scared. Make the group leader a much higher rank, and make some sidekicks with high rank too so that if the leader is killed they will take over. The courage of a group is determined by the rank of the group leader. Do not get bogged down in saying "but the leader would be a sergeant in real life", work with the game engine and make the leader a major.
2. You can't. This is the game engine being clever, and the loons taking cover as they move. Well that's what you'd do, isn't it? More courage might help, and more waypoints to keep them where you want them. However, the game engine is so good that it has flanking built into it.
The real problem is that you are trying to make them go an unrealistic way: rethink your plan of attack.