We need something that complements the innate jalapeñoness, and vinegar probably isn’t our best option. Something like lemon or lime juice might have the same problem, plus they would be so bitter we might have problems with oversweetening the ice cream. Pineapple juice would work well, but it doesn’t compliment jalapeno as much as lime would. Mango would be great flavor-wise but isn’t acidic enough. I think “pickling” them in a brine of either pineapple or white grape juice, salt, and a few milder spices is going to be the right way to go on this.
My bigger concern would be the effect of the digestive enzyme bromelain. Digestive enzymes break down food at a molecular level and can cause some unexpected side effects. For example, if you take a saltine cracker and leave it on your tongue for a bit, it will break the carbs down and eventually become sweet.