Zoe Saldana is the arguably biggest star among the cast so it's highly doubtful that she's going to get bumped by Alice Eve. Plus her romantic relationship with Spock has played an important part of both movies thus far and I can see them continuing in that vein for the third film at least.
Marcus was a redundant character even in STID, as pointed out by Spock. I liked Eve's performance, though I think she was largely wasted after Khan injured her, and I do hope they develop her relationship with Kirk in the third film, but I don't see that supplanting Spock-Uhura. Plus it would put a damper on the Kirk-as-horndog shtick that the new films are really playing up.
I think Uhura is the third spoke in the wheel, though I sort of agree with the idea that with Into Darkness, Scotty was the third most important character. With Uhura her importance was tied far too much, IMO, to her romantic relationship with Spock. She did help out on the Klingon planet and she did help apprehend Khan, which are all good things. But Scotty's disagreement with Kirk really helped frame the intellectual discussion that drove the film. I do think Zoe's Uhura is far more developed than Nichelle Nichols' but I do wish they would also imbue her with more intellectual/philosophical feistiness (sp).
While Uhura has likely replaced Bones they haven't allowed her character to be a pole of debate, discussion, or dissent like DeForest Kelly's Bones was. The films have her being either too lovey dovey, frustrated, or mad with Spock instead. She helps with the emotional aspects of the film and with the newer Trek films pushing bigger emotions, bigger everything it seems, I can see how that might have helped her character rise to prominence. It goes beyond mere marketing, though it certainly helps that a black Latina female is the third face on the posters and DVD/Blu-Ray covers and other promotional materials. It definitely sets it apart from previous Treks and has wider demographic appeal.