If digging around the roots is the main problem, I put 4-5 inch rocks around the base of all newly planted perennials and berry bushes. You could also use bricks or anything heavy, so digging won't disturb. Once the roots are established it usually isn't a problem. My girls have a 100' run, but still want to be with me in the garden and I appreciate all the grubs they eat, so I just have to figure out what works for each plant. I also plant any extra tomato plants in there run protected by large cages, so they can't dig them up, but when the tomatoes are coming on, they are allowed to pick their own. I also have pyramid cages so that when large groups of annuals are planted they have a week or 2 to establish and after that they don't bother them....unless, of course, they are tasty, then I don't plant those again. It is work and the pyramids were pricey, but so worth it as I use them to protect so many things....including broody hens and newly hatched chicks