seppuku question

The second was generally there as more of a mercy killing if I understand it correctly, to end the Samurai's suffering. I've read that occasionally the second would make the killing blow immediately after the Samurai made the first cut. Perhaps in this case it was considered to be a greater honor for them to end their lives themselves?

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In the ritual fashion of seppukku there would always be a second standing by to decapitate the warrior.
Generally the principal (who commits seppukku) and the second would agree in advance when to strike. Some would strike as soon as the principal reaches for the blade, some when the first cut is made, some would try to make two cuts and die slowly. But the second has to strike when the principal starts to show any discomfort (pain, crying, fear) to avoid disgrace for the principal.

The movie made just another huge mistake in portraying the entire death scene.

I guess they didn't want the possibility of another 46 men having to commit seppuku if they fail to chop their heads off.

That kind of bugged me too. I read that the one doing the beheading considered it an honor to be doing the deed.

Yes, it seems kind of odd in our society, but keep in mind this was a time and society where honor was more important than just about anything else (or else they wouldn't of avenged their master at all in the historical story).

While I suppose some of them could have died with dignity, I'd imagine some of them may have started to scream in pain after a minute or two, which is where the beheading is supposed to relieve them of that problem.

But my guess is that they didn't want to have to film 46 other guys standing next to them, because it wouldn't look as cinematic and what not, unlike the first one where it was just one guy and one of his faithful followers doing the deed.

Perhaps it was a deliberate thing. The scene may have looked too busy and cumbersome with another 46 blokes standing around.