I haven't done much slow pitch the past few years, but I will give it a go...
The result of an illegal pitch put in play gives the offense the option of taking the result of the play or a ball on the batter. Reading the minds of the players I could tell that the batter decided s/he would be out and saved the effort of running. The pitcher acknowledged the batter's decision to accept the out but in place of that take a ball. The end result is the next play, another pitch by the pitcher hit for a single by the batter. For statistical purposes, we should confirm the pitch count for the pitcher.
Having answered the question, IMO, this should never have been allowed to happen. First, the ball is in play, the umpire should vacate their position behind the plate and prepare for what should be a play made somewhere. This should help relay a message to everyone that something should be happening, and not another pitch since the plate umpire is not in position to call a pitch. If no one is moving, they are certainly going to look to you for guidance and using your mechanics to show that you are expecting a play should sink in, eventually, that someone needs to be doing something.
I had this happen in a U-18 fastpitch game this summer. It took at least 15 seconds of me standing in the infield between the pitcher and batter before a coach told a player to make a play/run to first. It was awkward, but you certainly can not tell one team or the other to do something, you have to let them figure it out. If, ultimately, no one does anything, you call time, award a ball on the batter and move on. The key to this is that it is obvious no one knows what to do or the rule. You will be explaining to both coaches what should have transpired, but I see no way to punish one team for the ignorance of both teams.