Welcome to the Forum! I agree with what the others said. Skin tags seem to get worse when your disease is active. Removing them during an active time is just asking for trouble. I had a few very small ones removed by a very experienced colo-rectal surgeon and had no huge problem, but everyone is different. I strongly suggest you only see doctors who are very experienced with Crohn's -- GI docs and colo-rectal surgeons rather than general surgeons. While people without Crohn's get skin tags, treatment for people with Crohn's is different and needs to be handled by a specialist.
As Habs mentioned, reducing irritation from toliet paper helps -- using a hand-held shower sprayer not only reduces irritation but gets you nice and clean. Sitz baths help reduce inflammation too -- 15 minutes in a hot tub (not the type that sits on the toilet). See a GI as soon as you can because there are various cremes and medications that can help reduce inflammation in your rectal area, and help heal fissues and reduce itching.