Did the people hiding him kill the girl because she wasn't hiding him well enough and they feel he would be compromised?
So they kill the girl and then put him back into the same hiding place again but all alone?
Why are they hiding him? He's a bad guy right?
They killed her because she was clearly too close to him and instead of keeping him hidden and protected, was being reckless (in their view) by taking him out to places he wanted to go where he would be exposed. The assassin took the General back to the same place initially, but they were moving him around from time to time.
The two leads were both very good in this.