The "Death of Audrey" sequence (really a reprise of "Somewhere That's Green") can be devastating for the audience, if it's played correctly. Mushnik and Orin are both very cartoon-y characters, so their deaths tend to land as part of the black comedy going on. Audrey's death, in contrast, is a sudden and real end of a character that the audience has come to love and understand. The audience should be grieving her right along with Seymour.
I still have fond memories of the original Boston sit-down production (Charles Playhouse in the late 1980's) with Carolee Carmello as Audrey. I remember always being very moved by her death scene, and the moment when Seymour would then gently lower her into the plant. Beautifully done.