Does there have to be some level of consent to kill characters off?
Well, there has to be "some level of consent" to do anything in a tie-in novel. Regardless of whether the idea originates with the author or the editor, everything in a tie-in has to be approved by the licensor as well as the editor.
Other than that, though, it's not like there's some formal list somewhere of characters you can't kill off, not that I know of, anyway. If there were still a Trek series on the air, then obviously any books set during the run of that series would be forbidden to make any fundamental changes in its continuity, including cast fatalities. But since all current Trek Lit (aside from the young-adult Abramsverse Starfleet Academy
novels) is based on productions whose onscreen runs are concluded, we basically have carte blanche. And there's certainly no reason why CBS would forbid killing off characters created specifically for the literature like Choudhury or Chen.