It's been said and said again in this thread... you basically have a choice of shelving it, releasing it as is, or doing something with the offending track (fading out and back in or dropping it altogether). If it's a critical show where no other copy exists, I'd say do the last option. If it's a run of the mill show, with nothing notable going on compared to others from the tour, chalk it up to experience and shelve it.
I've had to do this in cases where I've recorded an artist with permission, and most recently, with board access. The chattiness of the room made it impossible to do anything with the recording (and the stage mics pick it up clear as day); we then had a group of idiots up at the front yelling right by the front PA next to the omni mics we ran on-stage and then the hypers were back by the board surrounded by friends of the openining act who weren't there for the headliner but insited on yapping. Suffice to say, the sources of crap = crap.
You win some, you lose some. In this case, I'm willing to bet that it's just one of those shows just gets stored away; I just did that with the above-mentioned show.