It was probably deliberate that the Project Elrond reference was to the books instead of the films.
If you're going to make such a nice homage to Lord of the Rings, why not do it to the proper Lord of the Rings, namely the books and not the Hollywood film adaptations?
If you want to make the point that NASA is full of Tolkien nerds, why not make them real Tolkien nerds, ones who've read the books and not just seen the films?
The LotR films are more mass-market, so making references to them doesn't say as much. Everyone knows the "One does not simply ..." meme, for instance; but it takes a more knowledgeable Tolkien fan to be able to refer to Glorfindel at the Council of Elrond.
I mean, which one gives the "the head of NASA is a Tolkien nerd" impression better?
I would like my code name to be Glorfindel. You know, the name which appears in both the Silmarillion and LotR, even though it's only in The Peoples of Middle-Earth that Tolkien confirmed they're the same guy.
or something like
I would like my code name to be Gandalf, because Ian McKellen is cool.
This article entitled "The Martian is Cinema's Love Letter to Being a Nerd" agrees with my interpretation:
Watney’s excitement about the intricacies of maritime law and how it applies to Mars means he’s a space pirate because he’s a big ol’ nerd. Vincent Kapoor instantly gets why Watney wants to be called Captain Blondebeard because he already knows the intricacies of maritime law and how it applies to Mars, because he’s a big ol’ nerd. Commander Lewis (Jessica Chastain) is a big ol’ disco nerd. Rich Purnell (Donald Glover) is a big ol’ math nerd. Johanssen (Kate Mara) is a big ol’ computer nerd. Zhu Tao and Guo Ming, of China’s space exploration program, are the nerdiest nerds of all: Their “Screw the politicians, scientists need to stick together” moment legitimately had me tearing up.
The beating, nerdy soul of The Martian, for me, can be found in a single line uttered by Jeff Daniels’ character, Teddy Sanders, during a Certain Scene that will go down in nerd lore. (If you’ve seen it, you know the one.) If he’s going to take part in a secret meeting, Teddy says, “I would like my code name to be Glorfindel.”
The head of NASA, up until this point Teddy was the bureaucrat, the guy more concerned with public relations and funding than the science part of scientific exploration. With his suit and tie and his officious-seeming manner, he’s the square in the den of nerds. And then he drops a Lord of the Rings reference like it’s nothing. Because this man is the head of NASA. Of course he’s a nerd. He is the Lord of nerds. He is the nerd King. As a kid, he got teased for making intricate, cross-referenced charts about the grammatical rules of Tolkien’s fictional languages, and you know it.