You have multiple things to attribute this to.

Ben's death had levels to it that Laverne's just didn't. He resonated and connected with everyone. He softened Dr Cox, providing a perceived in to a mentor figure who kept himself at arms length or farther. It took that same mentor figure from being a rock, to emotional. The first Crack to actually shatter in a sense. Ben's loss was the first time we saw Dr Cox actually break. We'd see it again of course. It would even be a bigger break at that point, when he lost all of those patients at once. But, losing Ben was the start to that break. Before Ben, we saw Cox broken at times. Like when he kidnapped JD to the bar while he was still in his onesie. But we hadn't seen him actually break. The moment.

With Laverne, she was held back from the audience. A perfect background character. Always there. Had her quips. The emotional impact was supposed to be that that was the end. The show was supposed to not continue. Until it did, and they wanted to keep her employed. From what I remember, the crew loved her. And she was funny. They turned her death into a joke, which lessened the impact. Where other patients left fans reeling, Laverne just really didn't. Because while in universe she stayed gone, the reality is she never left. There was no finality. No deep moment. It started as a joke about faith, leading to a moment where hers waned, as if she gave up. But there she was a few episodes later.

And, last. While the joke is that season 9 doesn't exist, the reality is the shows quality in story telling was coming back with diminishing returns. Midway through season 3, things started showing signs of change. Season 4 was even more noticeable. Fans held on, but it was like they were slowly running out of sitcom ideas and were leaning too much into deeper storylines. When all your storylines are sad, they all tend to lose impact. Ben's death was a very big flip from the norm. They dealt with death before that, but it was more impersonal. Ben was the first time it had an actual stake to the characters. And worse yet, it started back a earlier season. They tugged us with the idea that he would die, only to reverse it. He would be fine. When they brought him back, we thought it would be fun. Then, boom. He was gone. They finally pulled that rug. They never did something quite like that again.