Okay, this is a great example of what happens in D1. This crew handled it well, I say crew because three guys worked to keep the offender off the field, the assistants at bay and they resumed play quickly.
I don't worry about the penalty - submit the form and contact the proper administrators - let them handle it. NCAA ball has penalties that vary according to the offender's history. If this was his first offense, he'll likely get an additional game suspension, that is all. He thrust his bat at the PU but did not make contact and immediately walked away - in fact, he was retreating when the incident occured. Further, he barked a little in the dugout, but then went into the team clubhouse pretty quickly. The only audio I could hear from him said 'That was horrible.', but he probably dropped a "darn" or "heck" in there somewhere.
The PU did a nice job and handled a catcher (who should know better) very well. For those who still don't think that a good D1 crew couldn't possibly handle anything higher than that level...