Maggots can and do eat through healthy skin. I have much experience, sadly, of removing maggots from entire litters of orphaned wildllife. Damp, compromised skin, especially if covered in excrement, is a perfect place for maggots. If there is just one hole, drip hydrogen peroxide into it and stand by with tweezers until the maggot becomes visible. IMPORTANT to KEEP REPEATING until you are POSITIVE there is not even ONE left. If you get them ALL, the wound heals rapidly. If it doesn't look better in two or three days, check again with hydrogen peroxide, to make sure that none were missed. As a previous post noted, carefully examine her for fly eggs--FREQUENTLY!!!! On mammal babies you will find them in the creases where limbs join the body, in the anus and urinary opening, umbilicus, behind ears, and in the corners of the eyes. You will notice all mothers pay particular attention to grooming these areas on their babies. They keep the fly eggs removed. Once Mom is removed from the picture, the eggs remain, hatch, and start eating. Where they eat, they also produce waste. Waste further breaks down the tissues, and the feast goes on.
Frequent betadine rinses or flushes are safer than ointment. Ointments are fine for wounds that are open, but deep wounds or wounds with tracts (tunnels) with a small opening can harbor bacteria (including those that cause gangrene.) If you seal up the top of the wound, or allow it to self-seal before the deeper parts heal, you set up conditions for anaerobic ("no-oxygen") bacteria to grow. That's why Mom (and Doctor) always told you NO ointments on puncture wounds! FAR better a draining wound than a sealed, bacteria and fluid-filled wound.
Any animal with excrement on the skin needs to be very gently cleaned and dried immediately. Even daily is not really enough to avoid damaged skin. She's been very "lucky" up until this point. Ammonia-burned skin is VERY painful. It may be worth assessing whether you are doing her a favor by not "dispatching" her, if you're not able to solve her diarrhea problem. I'm not suggesting that this would be easy.
One thought; there are products on the market for people with colostomies, to protect the skin under the colostomy appliance ("bag".) These wipes provide a barrier between the adhesive and the skin, and also protect the skin from wetness. Check with a nurse in your area; if you can get some, and it DRIES without stickiness, applying it immediately under her vent may protect her skin from ammonia burn, and also make the excrement easier to remove without damaging her skin.
Glad you caught the infestation in time; good luck!