I have used a basting gun, but I would not recommend it if you want to hand quilt. Your quilting thread will catch on all the little ends sticking out.
Have you considered spray basting? This would be faster than using a basting gun. I have not tried to hand quilt with a spray basted sandwich, but I'm pretty sure I have seen posts from hand quilters who do this.
Addendum: Are you thinking of doing the gun basting from the backing side? I am thinking the tabs would not interfere so much with hand quilting if they are all on the back.