No, I don't fear hitting friendlies. Remember, there is no such thing as friendly fire. If the sight picture isn't good, you don't take the shot, unless you have no choice. Then you shoot to stop.
That's the good thing about shotties. You should normally get a shot. The biggest worry is that you will have to fire to stop the BG from hitting friendly targets. Otherwise, you should not have to shoot.
Shotties don't miss, and seldom fail. Tac lighting, good manouverability and good patterning are all important. If the shotgun is coming out, it is because it is very necessary. If it is necessary, then odds are you will need to fire it. Make your shot count. Rechamber. Is target still a threat? Scan your sector.
Disarm the subject and secure his weapon. Scan your sector. Check your six. Turn on lighting. Call emergency services.
In the meantime, your friendlies would normally be behind you, and you in a position to guard them. If it isn't that way, then you need to reevaluate your positioning. Maybe you need to move, or rearrange the furniture, or whatever. But you should be positioned between the threat and who you're protecting. Know your target and what is beyond it. Practice.
Trust your feelings. Use your instincts. Don't be afraid to feel some hate. It may save your life. I used to be a peace loving idealistic young man who wanted nothing more than to play guitar and love everyone man. Now, I'd pop an intruder for looking at me wrong. Criminals cross the street before they walk in front of my house. I live in a real high crime neighborhood. Luckily for me I haven't come home to find anything of any real value missing.
Alarms, dogs, early warning systems. All good. See it as a fight, a battle, prepare for it, fight to win, fight to live. Friendlies should be the last thing you worry about, and the next thing a bg has to worry about, should he make it past you.