Rem threatens Light by saying
If you try to harm this girl, I will write your name in my note and kill you.
Six months after Rem threatens Light, the killing spree has begun again as soon as Misa was released. Because of this L assumes correctly that Misa is the second killer. Rem knows that if she doesn't take action Misa will be killed soon and she also realizes that this is exactly what Light had planned. Therefore she considers killing Light as she had stated six months earlier, but by now she realizes she can't kill him. Her statement wasn't a bluff, she just realizes that there would be no point on killing Light. On the contrary, and I quote:
With this, killing Yagami Light means nothing. Misa cannot be saved.. More than that, Misa will be lost as an ally and I will be driven more quickly into a corner... No. I already know that if Yagami Light dies, then Misa will lose all will to live. Yagami Light is already a human who is in many ways, necessary for Misa to continue living...
Rem had played her cards well, but Light played better. He had completely manipulated the situation, resulting in the death of a Death God. If Rem wanted to save Misa, she had to kill L and had to do so quickly. As much as she might have hated Light, killing him would result in the complete opposite of what she wanted and would make her death an utterly useless sacrifice.