Even though Tyler is part of the Narrator, that part (which we call Tyler) has an agenda, which we see represented as Tyler's proactive "teaching" of the Narrator. You've touched on this in your question:
Tyler didn't want The Narrator to realize they were the same person because The Narrator didn't have the balls to do on his own what Tyler did.
If Tyler didn't want the Narrator to be aware of the split personalities, why on Earth would he trust Marla with that same knowledge, which gives her the power to ruin Tyler's agenda?
Note: your question seems to imply that the Narrator's realization (about Tyler) is the biggest problem for Tyler. It is not. It is a problem, but there is a threat of something much more dangerous to Tyler: a psychiatric hospital and anti-psychotic meds. The Narrator's knowledge about Tyler is only an obstacle (to Tyler's teachings), but the hospital and meds will drive Tyler out completely.
Marla being aware of Tyler being the Narrator (or vice versa, I guess) means that she's in a unique position. The guys in the club generally think of the Narrator as a guy with some serious balls (= Tyler), but they don't realize that it's a matter of split personalities.
As such, Marla is the only one who can really pull the emergency brake, call in a psychiatrist, and put an end to Tyler's agenda. This is why she's a threat to Tyler.
And there's a great duality here, because before the Narrator realizes he is Tyler, he interprets Tyler's words differently.
- Pre-realization, he can interpret Tyler's words as Marla being dangerous because she knows too much about the fight club and its dealings.
- Post-realization, we now know that Tyler thinks of Marla as a threat, because she can put a stop to the psychological manifestation that is Tyler (or at least his agenda).
Just a realization. Tyler seeing Marla as a threat indirectly confirms that Tyler knows he's inside the Narrator's head, even though the Narrator himself is not initially aware of it.