In episode 20 of UBW (or episode 8, UBW 2nd season), Kirei announced that he would take Rin's heart. I suppose that he wanted to use it as some sort of vessel for the grail.
But what about Illya's heart that Gilgamesh had taken earlier? Why did he take Rin's if he already had Illya's, which I guess is better?
Perhaps he was not allied with Gilgamesh anymore? Or perhaps, he just wanted to kill Rin for the laughs and giggles?
In episode 20 of UBW (or episode 8, UBW 2nd season), Kirei announced that he would take Rin's heart.
First, that was episode 19. Second, he says complete opposite thing. He says
"The vessel has no need for a heart." This implies that he wants her body except her heart.
In episode 20, we see what he meant, when
Gilgamesh pushes Illiya's heart inside Shinji, turning him into vessel and using him as way to "anchor" the grail to this world.
The reason for this is that
Grail needs two components, first it needs the core. In Fifth grail war that is either Illiya's or Sakura's heart. And it needs a vessel to anchor it to real world. Vessel can be any body with enough magic circuits. Normally, Illiya herself works as both core and vessel, but for some reason Gilgamesh didn't want that, so he only took the core. And at the time, Rin is only actual mage nearby, making her best option for a vessel. But when in episode 20 she regroups with Saber and Shirou, he could no longer get to her, so he went with next best option : Shinji. Even though his magic circuits are pretty bad, he is still a magus.
Seriously, it may be a spoiler, given that the status of Gil/Kotomine's alliance is pretty uncertain in the anime (if you do not have complementary information).
However, taking it from cues mostly from the anime:
So, that suggests that whatever part he envisioned for Rin, it would not need Rin's heart. I guess you can take it from there.
Going from that, I believe that the intended meaning of "I will take this heart." is that he is taking Rin's heart out, but not necessarily to make any use of it.
