It is important that the student leaders are not determining the penalty, but only accessing what has already been laid out in your policies. If you tell the band that if you forget your water bottle you run two laps, then the section leader can be the one that assigns that. What they should not do is make up their own penalties, or if the student leadership decides before the season on a series of penalties for rules infractions you must approve it and do it publicly.
The other thing I used to do to help ease the potential hostility and help keep the student leadership somewhat in check (we all know that they are WAY more punitive than we are) was the policy that the student leaders did the penalty with the 'offender'. The student leader runs the laps with the person that forgot their water. Students that were late for inspection before a game tidied up the band hall afterwards WITH the student leaders. This also reinforces the concept that the actions of their section - good or bad - are in part their responsibility.
To reiterate - this is very much variable from school to school, and you should absolutely sit down with your principal first to determine what they will support. If the first time they hear that the flute section leader 'made' a freshman flute player run laps per your policy is from a parent, you have a big problem.