Although I do not have a source to sight at the moment, one thing I remember from studying law enforcement in college is an alarming amount of officers who are killed are found with there gun still in their holster, often with evidence they tried to draw, but had not unbuttoned the strap. Police are trained when to loosen the gun in the holster, when to have their hand on the gun, and when to draw for very good reasons. Unfortunately, since a large percentage of the people they deal with are not a threat, they can get relaxed and that is when most officers get killed.
The police response stated that a man on deck was order to stay on deck, but failed to follow that order and went below. To me that is reason to draw your weapon. They do not know who these people are, what they have on board, or why this guy refused to follow the order. No one was shot, no one was hurt, personally I think people take to much offense when police put their hands on their guns or draw their weapons. "What know of person does he think I am?" is an argument I hear a lot, but the fact is he has know idea, and most people who do shot cops do not have a "I like to shot cops" tee shirt on.
They did not draw weapons because they thought there was a sewage discharge issue, they boarded to do an inspection, which included a discharge inspection as well as other checks I am sure, and drew weapons because someone disobeyed orders and went below.
All that said, I do not live in Florida, have never boated there, and have not had this type of boarding occur on my boat. I can understand that the LEOs are likely getting way over zealous as I have seen several reports here about situations that seem way over the top, but this does not seem like it was really all that out of line, except perhaps the boarding while underway. Even that I have mixed feelings about. I would like to have a "heave to and prepare to be boarded" notice, and a few minutes to stop the boat, however for other people that would be a few minutes to hide / dump all the illegal stuff they have on board. If you want to catch the guys breaking the law, you can't exactly just sit around patiently waiting for them to destroy the evidence first. However, I must admit that if I was boarded with no notice while underway, I may have other opinions.
One last minor point....
"a .45 caliber automatic weapon drawn and pointed at my chest" Handguns carried by police are not generally automatic weapons, so ether it was not an automatic weapon, or it was not a holster-able weapon, in which case it would logically be in his hands, or over his shoulder which would make it totally useless. The police report says "draw his duty weapon for officer safety purposes" so likely this was a handgun, and not an automatic. Minor point I know, if you are shot, it really does not matter if the gun was auto or semi-auto
Ok, one last last point...
"yet I was given a citation (under gunpoint) " Where they really still pointing guns at this point? That does seem way overboard if they where, or was this just for dramatic effect, because they had guns on them. I can not see them actually point a gun at him while handing over the ticket, but if they where, that's just nuts.