It sounds like Mary Alice may have left in a mutual decision. She didn't give many interviews about it that I can find, but there's a 1990 piece in the NYT about her theater work where she says she'd felt like she'd sold out when she took the job, 'even though I hadn't,' but then basically said it wasn't all it was cracked up to be and that 'the first shows' were good, implying the rest of the experience was less satisfying for her. Which is too bad, because I enjoyed her on the show. But one way or another they did phase her role out in Season 3, which I'm bingeing now where the dorms go coed and Jaleesa and Walter take those elder roles. (They also break Jaleesa and Walter up around this time, I believe, which Dawnn Lewis says they did because she and Sinbad felt their romance had seriously limited their stories and fought to get out of it.)
I do think keeping Denise and Maggie in the ways Allen's always talked about would've been fascinating for the show, but also would've left it extremely altered from the quiet hit it became. I'm not sure how characters like Kim or Freddie or others could've found real estate and airtime to exist, let alone how Whitley evolved.