I'm trying to lose weight, but I'm afraid that I might permanently damage my digestive system. Any thoughts?

Weight loss is good. There is not any significant risk to your digestive system from weight loss. Starvation or rapid weight loss can cause fatty liver. Many weight loss supplements, in addition to being ineffective, have compounds in them which can occasionally cause liver damage. Low carb diets can cause constipation and other health problems.
Depends. There are so many diets. I would recommend a physician program to get the right combination of medications and nutraceuticals to suppress your appetite without effects on your intestinal tract. The danger is when you use the stimulant laxatives, than your colon will undergo changes and not work correctly. Also, if not eating correctly can lead to stress and possible gastritis and ulcers.