To be blunt, it's not the filmmakers' job to "pay homage" to any given actor, no matter how important she was to the past franchise. It's their job to tell a story that works in and of itself rather than just as an exercise in nostalgia. And that means using characters in ways that serve a purpose in the story. Movies don't have as much room as series TV to flesh out supporting characters, so they have to limit themselves to the supporting characters that contribute something useful.
And let's face it, our feelings about the actress aside, Chapel's importance as a character isn't all that great. The only thing that ever really defined her aside from her job as nurse was her crush on Spock, which doesn't fit into the new paradigm with Spock in a relationship with Uhura. She was in fewer than 1/3 of the series' episodes and never played a major role in the movies except maybe in TMP. The fact is, she's expendable. At least they mentioned her, which is something.