I think all you can do is be patient. She will overcome her fear on her own when she realizes she's safe again. Encourage her not to quit playing soccer and let her know its okay to feel a little scared. Paying too much attention to her fear of the ball might make her more timid. You really can't force her to be more assertive, its something she needs to come to grips with on her own and it will happen it just takes some time. My daughter is 9 now, and has been playing for 4 years. There was one year where she was hit in the face really hard bringing her to histeria.
She was always an aggressive player and I noticed her playing changed after that incident. It took about a year I would say until she was back to her normal game.
Also, I figured as they get older, they play harder and injuries are more common as well. She never expected to get hit that hard ever. Playing when they are five is much different that 7-9. Kids are more serious players and more aggressive and that might make her a little nervous about getting hurt too. I played soccer for 8 years myself and think that there will be a day when she will play like her old self! She just needs her condfidence back in that she won't get hurt everytime she runs after the ball.