that wormhole scene has no adequate defense.
Well, the point is to unnerve you, and to make it clear that you're not even remotely in the same place anymore.
It interesting to compare it to the wormhole sequence in Contact. In that one, the aliens have humanity ...for lack of a better word - I just mean that they have feelings and want to connect with us on that level. "The only thing that makes the emptiness bearable is each other" they say. They try to make everything as comfortable as possible. Human engineers mount a chair in the pod, so it's a bumpy ride for a bit. But as soon as the chair is removed, it's smooth as silk.
By contrast, the aliens in 2001 aren't sentimental. They're curious, and they're not malevolent, but they're not caring. The idea that human company "makes the emptiness bearable" wouldn't occur to them. It'd be like suggesting that an insect makes your life bearable. As a scientist, you would find the insect interesting, but have no desire to commune with it.
The Aliens in 2001 collect Bowman like we might collect a bug in a jar. The sequence is supposed to scare you. It's supposed to be clear how much energy is being used, and how far you're being taken. You're supposed to be screaming for it to stop - there are even shots of Bowman toward the end of the sequence where he's screaming, but we can't hear him.
Something I strongly recommend everyone to do is to watch 2001 in a dark room. A proper theater would be ideal, but at least watch it in the dark. Before anything is shown on screen, there are two and a half minutes of music. This sequence represents "everything that happened in the universe before we existed" - when someone pointed that out to me, it blew my mind. The music starts off serenely; relaxing. We're comfortable with our narrative about the big bang and so on. The fact that that happened in the past doesn't bother us. Then the music changes (it's when the oboes start) and that's supposed to unnerve you. Stuff is clearly happening - not natural stuff - but you have no hope of seeing it because you don't even exist yet.
You can only pick up on the feeling of that if you watch it in the dark. It's great.