Maria is smart enough to know Yuda's more of a liability than an asset. He's too unreliable and unpredictable to actually be of use, and as he is right now he's just one more avenue of attack for her to watch.
Kinugawa has survived for so long due to all these complications in Maria's revenge. I thought for sure he was the next to die, but it's been so long since Shikimi kicked the bucket. Of course Okaya is no idiot and he knew investigating Kiritaka's parents would be his lead to whoever wanted them dead... it's just a matter of time until he finds out, and that's why Maria doesn't have the luxury of time. She needs to act soon before they start coming for her.