I am going to not respond, as I do not want to ruin what would have been a nice a balanced debate between me and Britophile.
Britophile - Senna always felt FISA greatly favored Prost, which was ironic given that Prost felt Honda favored Senna. It was flawed logic that the pole sitter would be at a disadvantage, so I can see why Senna was angry and the memory of the incident the year before sent him over the edge, still I am not condoning what he did.
Also, Senna had a long standing grudge due to Monaco 1984, where he felt Pros was favored by the system as well.
A lot happened between both before Japan 1989 though, from both sides. Prost himself admitted as much, and even took a share of the blame, which is not shocking as he like Senna, was a class act all in all.
Monaco in 1984 was a tricky one too, I agree. Ironically if the race would have continued neither Senna nor Prost would have won it. It would have been Stefan Bellof's race all the way.
Toleman reported that because of an earlier mistake at the chicane on the waterfront, Senna damaged his suspension which would have forced him to retire in no more than two or three laps time. And the reason why Prost was so slow because he had the very same brake problems that caused Lauda to spun off a few laps earlier. There's no doubt that Senna would have caught him in a lap and there's no doubt that they both would have retired soon afterwards.
The reason why the race was red flagged is ironically also because of Bellof and wasn't beacuse of Prost or Balestre. It is a little known fact that Bellof was also driving in the World Sportscar Championship series for Porsche that time and his teammate there was the seasoned veteran Jacky Ickx. Ickx was getting a massive salary for the drive as he was the lead driver of the team. Bellof on the other hand was driving for free, mainly because of his inexperience and also beacuse of contractual reasons as he primarily was a driver for Tyrrell in F1. Ickx was an appointed steward at the Monaco GP in 1984 and he realised that he would lose face massively should Bellof won the race. After all, that rookie teammate of his was driving for free and still he was the one looking to win the prestigious Monaco GP. He was by far the quickest man on that horrendously wet track in a massively underpowered and inferior Tyrrell - he was catching Senna in an even faster rate than Senna was catching the struggling Prost.
So Ickx desperately decided to suddenly red flag the race on lap 31 and in fact he never discussed this move with other stewards or with the FISA representatives before doing so. He acted on his own purely because of personal reasons. Later on he attempted to hide the real motives behind his actions and tried to sell the story in certain circles as by stopping the race he just wanted to be a good sport for his employer, Porsche because that way he could secure the victory for the company as McLaren was powered by TAG-Porsche engines back then. He failed miserably though and Balestre was furious with him. Ickx got his steward license suspended and he also had to pay a fine to FISA. Even months after the race it was a touchy subject in the paddock and as a result Ickx would never have any appearance as an official in a F1 race ever again.