Completely agree with you.
I think what makes this film and Schindler's list so disturbing is how Steven Spielberg made us have the same emotions as the ones we see on screen.
When Spielberg wants to he gets the best performances from his cast.
Probably I'm comparing this with Schindler's list way too much because I saw Both this weekend and I have them really fresh on my memory.
Another coincidence with SL and Amistad is that we see a hero who evolves and changes as the film goes by.
Mr Baldwin( Mathew McCounaghey) first takes the case for prestige and having a good name in his profession but latter he starts to really care for the slaves and fights for them till the end.
In Schindler's list Schindler(Liam Neeson) starts to employ them because he needs them for his business but latter gets way to involved with them and does everything he can to save his workers.

I agree, the worst scenes for me to take were that baby - the woman with the baby in her arms who just leapt from the ship to take their lives. I understand why she did that, it's just still really hard to watch. It's just the fact that there was new life on that ship and either way they were all still completely beep
Also the scene where the slaves were all chained together and thrown overboard to drown because the ship was too heavy.
"Hey guys! Whoa, Big Gulps huh? All right! Well, see ya later!" Dumb & Dumber

He wasn't vilified just because it was a religious movie.
The disturbing scenes in Amistad are much more earned than in The Passion.
Anton Chigurh is dead and Spider-Man 3 is superior in every way to Funny Games.

This is what made The Passion of the Christ so effective. Gibson didn't sugar coat Jesus' scourging, as has been done in earlier works. Of course Gibson was vilified or this but that's only because it was a religious movie.

I know it's realistic but still very disturbing.

I don't think it's fair to say "too many". Spielberg definately made the slave massacres about as realistic as possible. I agree that they are probably the most disturbing scenes you will ever see in any Spielberg film, but that is what makes the film so effective.
Schindler's List
was orchestrated in much the same way.

"What I want to know is how we're going to stay alive this winter."