As a kid I was fascinated by that track. It sounded truly evil, very different from anything else in the game. I don't recall finding it ear grating, I guess because I was hearing it out of the GBC's tiny speaker.
Listening to it now, I can see why people don't like it. The sound channels are all off-key by different amounts, clearly done on purpose, which is an odd choice. I think they were trying to get the GBC to "realistically" replicate a style of music that it just isn't capable of. The HG/SS version makes it a lot more clear what they were going for.
It has a cool beat though, and I dig that bassline. With some changes it could be more enjoyable to listen to. For one thing, the weird tuning could be fixed. The wave channel (bass) is playing very harsh waveforms that give it an overly buzzy sound, that would be an easy fix. The pulse channels are set to the rather unpleasant 12.5% duty cycle, I'd set one or both to 25% and give them a slight vibrato so they don't sound so stagnant. I'd also add more percussion so it's not just that single buzz sound over and over. It's probably possible to hack the ROM to actually make these changes, but that's beyond my skill level.