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To be clear, in the manga Irene was not concerned about her lack of arms, saying that fate makes its own plans or something like that (mainly as a reference to the fact that she didn't need to fight anymore, and the arm was given to someone who could make use of it). In the anime, she made the comment that even with both arms she'd probably have a tough time fighting Rafaela.
As for why Rafaela was there, it had been close to two weeks since Clare was supposed to have met up with Ophelia for the hunt (1 week asleep plus at least several days training), and no word had come back. Rubel undoubtedly had her go check things out. The only question is whether he had any particular standing orders for Rafaela regarding Irene, or if Rafaela was simply carrying out the existing execution order.
Rubel being one who plays his cards very close to his chest, I suspect he wouldn't be giving special orders that could easily be traced to him. He might give 'suggestions', though. While Rafaela generally seems to be pretty heartless aside from her issues with her sister, she was still relieved when she found out that Teresa didn't have a sister (and was thus not part of the soul link experiments). There are still a few small windows of opportunity to allow for Irene to still be alive, but we have nothing to either support or disprove whether those windows exist. Until then, Irene stays cuddled up with the cat, both alive and dead at the same time.
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