If you cant remove the female to another tank where she is protected and you want the fry to survive then you will have to put her in a floating breeding trap. I often find that as you lower it into the water the guppies become curious and come see what it is and often they swim into all by themselves. Whether they become stressed depends very much from birthing to birthing and from female to female but i have never known it do any real harm. One tip though when she is due to birth leave the light off. Also make sure the trap has alid as other fish can and do sometimes jump in with the female and munch away on the fry to their hearts content