I would have gone right back to the museum ticket staff and told them very politely but firmly that the group was so noisy and active that you were unable even to hear the audio tour and that you wanted to leave and return after lunch that same day and expected to do so on the same ticket (no extra cost to you). I bet the museum would have accommodated you; they were well aware how loud and obnoxious this group was, and museums generally are in the business of pleasing the customers, not running them off. I think if you'd nicely emphasized that the group was not just making it crowded -- no museum can really help that -- but was overriding the audio tour right in your ear, you would have gotten an apology and a later time slot.
I bet this is a very popular exhibit and has "timed entry" but they would have tried to help. Was your initial entry, the one where you were asked to wait an hour, a timed entry -- where your ticket said "enter at 10 a.m." but you were asked to wait until 11 or something along those lines? In that case I would have told them that I had a timed ticket and had based my transportation and parking on that time and could not wait, and expected to be admitted at the stated time.
If you did not buy tickets in advance but that day at the door, then the museum was within its rights to ask you to wait if the exhibit was very crowded. It's possible that due to fire codes they simply could not admit you at the time if the exhibit area was at capacity.
I hope you won't blame the museum, which sounds like it was overwhelmed that particular day. I'm sure the staff was mortified at this group's behavior. You could write an e-mail to the museum (look at the web site for the appropriate contact) and note that the school group created a serious obstacle to even seeing the exhibit, much less enjoying it, and ask that in the future they might let patrons know when a school group is going to be there. But to find that out you'd need to call in advance of your visit rather than turning up. Still, worth a call, if they could let you know.