In hindsight, rewatching the scene where "Prince Ali" is captured and tossed into the sea makes no sense.

First of all, how the hell did Jafar know that Ali and Jasmine were going for a carpet ride?

If we assume that Jafar had some kind of surveillance magic which meant he could keep a tab on Prince Ali, then he clearly wasn't watching Ali when he was talking to the genie or when he and Jasmine revealed that Ali is actually Aladdin. Otherwise, why doesn't he know about the lamp until he sees it on Aladdin's person? And if we assume he just happened to notice Ali and Jasmine either leave or come back, then it still doesn't make sense. Seeing them come back, Jafar would have to quickly assemble the guards, give them some kind of explanation, and then set a trap which would be in total keeping with Ali floating down to the ground on his carpet.

Secondly, what the hell is up with the guards' mentality??

The guards are clearly violent, but they've only been shown to be violent when dealing with criminals. They never commit crimes of their own that we know, and Razoul treats Jasmine with incredible respect when he recognizes her, even to the point that he doesn't even protest Jasmine's order to release Aladdin. He just meekly deflects her off to Jafar. As far as we see, the guards are only doing their jobs, albeit brutishly. So what the hell did Jafar do or say to get them to go along with capturing a royal visitor from another nation, assaulting him to the point of unconsciousness, and then throwing him into the sea with intent of murder? They clearly don't know it's really Aladdin, and they show no signs of hypnotism. So what the hell made them think that doing all that to a prince was a good idea? Jafar is not the be-all end-all authority, and they know the Sultan likes Ali, so what was going on?!

And also, can you imagine how horrified they'd be to see him return the next day and be named as Jasmine's groom? They must have been packing up and fleeing town when they saw him alive and well! And at the end of the film, Aladdin is STILL engaged to Jasmine and he will become the next Sultan. Can't imagine he'll be too forgiving of those guards (I'm choosing to ignore Aladdin's relationship with the guards in the sequels and series because there is no way in hell that he'd just forget that they tried so hard to kill him). And speaking of the Ali's status...

What was Jafar going to say to the Sultan or Ali's family?

Remember, Jafar did NOT know that Ali was Aladdin until he saw the lamp on Aladdin's person. As far as he was concerned, he was ordering the kidnapping, assault, and murder of a prince. Sure, he was suspicious of where the guy came from, but the prince is clearly rich and powerful based on his entourage. What if Ali really WAS the prince of a foreign country? A country that was more powerful than Agrabah? Was Jafar just gonna shrug and say "Prince Ali left!" to them too? They won't like that explanation any more than Jasmine did, and for all Jafar knows, they have a huge army ready to conquer any nation that insults them.