You don't understand dramatic setup.
The transporter malfunction serves to set up that there are potentially real and life-threatening consequences to rushing this ship out. We can be told this film is about "show, not tell." That we've seen one deadly malfunction before raises the stakes and the tension amongst the characters, and creates additional anticipation when they turn on the warp drive. In a film criticized for lacking in dramatic moments your decision to excise one is, frankly, baffling.
But doesn't the wormhole sequence show this as well? Not only that, but the wormhole scene has McCoy directly saying that Kirk is pushing, almost gets the whole ship destroyed due to Kirk's lack of patience/familiarity with the situation, and results in Decker showing him up. (This is all aside that the wormhole scene would be very hard to cut while keeping essential character scenes for Kirk, Decker, and McCoy).
It doesn't create anymore stakes though: it's fixed with barely a mention and is never referenced again, the depressing of Kirk and somber atmosphere it develops is quickly brushed aside. Scotty's word (a word that viewers had come to trust over the years given his miracle worker status) should be enough. I realize that in cinema it's preferable to show and not tell, but it's also important to be economical with your story telling, and we do not need multiple scenes trying to tell us the same thing, especially one that is so isolated. The same problem applies to the V'Ger exploration scenes... in the words of SF Debris, they mostly say the same thing: this is a big ship.
Because I'm verbose, I'll make one final argument:
Wormhole was setup by Scotty before launch, after the first captain's log, by McCoy, and pays off with arrival of Spock, dressing down of Kirk by Decker and McCoy, and a happy moment where the ship goes to warp. It has functions to further the story, characters, and atmosphere.
The transporter accident was setup (partially) by the SF scene and one line during the pod ride. It's payoff is the end of the scene where Kirk looks upset, and has Decker pull double duty (which makes D more upset). That's it! As I mentioned, this scene could be entirely removed (along with the original conversation at SF) and one would miss nothing that has not been conveyed already or conveyed after: Kirk is being bullish, Decker is mad, the ship needs fixing.
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"First, Kirk's picking Sonak and then his reaction to the accident ("I'd still like a Vulcan there if possible") makes it clear he wants Spock. That's telling the viewer about where his character is and what he needs. It's tied to the whole theme of the movie: of characters desperately searching for the thing(s) that will complete them.
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Third. Continuity We've seen people beam from transporter to transporter before ("Tribbles") and since (ST3, ST6, etc., etc.), so it's not like it's out of left field.
Your first point is valid, however I think this could be conveyed with some clever editing and re dubbing of the SF sequence. I'm currently looking for suggestions on how this could be done.
I agree, it's not unusual, however we are never told that the transporter is fixed; the fact that engis are shown working on it while it's in use makes no sense when you consider they could have just as easily not used the pad and avoided any unsafe situations. The transporter is probably one of the most reliable technologies we are shown in the course of Trek, which makes this situation seem even more odd when thought about: either what we were shown wasn't true, or the Enterprise personal are incompetent (though this counters what we know to be true as well).