I was also diagnosed with indeterminate colitis...and also stayed indeterminate after surgery and several additional tests (inc. one very expensive one we had to send out of state of which I can't remember the name.) I was fine with IBD meds and a bi-annual flair that required steroids until I wasn't fine and then it was toxic megacolon almost overnight. So I didn't have a choice of anything initially. They removed my colon and gave me a temporary end ileostomy and left the rectum in place and then said wait to heal and get healthier before follow-up surgery.
While waiting and healing I ended up developing what my doctor determined were extra-intestinal manifestations of the disease, including pyoderma gangrenosum around the stoma site which made it all but impossible to adhere an ostomy bag. So the decision was kind of made for me -- I had to have the j pouch surgery.
I had a whole slew of problems during the 5 years I had the j-pouch (incontinent ileostomy) and now have a k-pouch (continent ileostomy.) One of my first surgeon's prescient responses I recall from after the surgery was that the worse a patient's disease is before the surgery tends to correlate to worse experiences after surgery. The medical community is still learning so much about the disease and he simply acknowledged that early difficulties can in general be an indicator of difficulties that will often manifest later in his experience. My personal experience also confirms this statement -- the people I've personally met who are living well with j-pouches and little if any problems all had UC and all had the j-pouch surgery by choice, before the disease progressed to toxicity.
Given both your indeterminate diagnosis and your conflicting doctor opinions, I would suggest you consider getting a second surgical opinion and/or ask your surgeon about just having the colon removal surgery and temporary end ileostomy at first. Then you could evaluate what life is really like with the ostomy bag, as it is understandable that some people have issues beyond health reasons for not wanting one. If you don't have an issue with it and you continue to have other problems (fistulas or inflammation) in that area, you could forgo a lot of pain and problems by just having it made permanent. Or, if you do NOT want to stay with the ostomy bag and do want to try the j-pouch, then you can have that created and healed before "take-down." I will note that many doctors actually prefer the multi-step procedure, but it is understandable that most people want to avoid an extra surgery and eliminate a step.
There is also the k-pouch to consider -- which is what I was revised to after a j-pouch. With this style of "system" you still have the internal bag like a j-pouch instead of the ostomy bag, but could also have your rectum removed for one less potential problem site. It entails defecating by means of intubating a continent stoma on your belly instead of rectally so it is a big change. Again, this would likely necessitate another surgical opinion, but that would provide you with some valuable insight if you were able find someone. Pertinent to your current issues, you will likely get some good information here at j-pouch.org searching for posts from j-pouchers with perianal fistulas -- I know there are a lot of them.
You will also find an overabundance of posts here about liquid stools and frequency -- everyone is very different. I will say the following in general: Most docs seem to be okay with more bathroom trips than the average patient -- I think the doctor version is 8-12 times per day is okay but patients are generally trying to get down to 4-6. Also, in general, everyone is very loose at the beginning and this improves with time -- the diversity is in how loose for how long. And lastly, diet is also a factor, with some things being more universal and others more variant from one person to another. While these are second to your main decision, you will also find many, many posts here on all these topics.
I wish you the best of luck and lots of blessings on your journey to an answer, Jennifer