See, there is a difference. There will be survivors, and Dakken isn't a shark on two feet that kills anything in its path, like Victor Creed. He's sadistic and cruel, but people live through it. Logan feels Dakken can be redeemed, and everyone in the room has a fighting chance against him, one-on-one.
Wanda, at this point in time, is a reality warper, who may kill anyone of them on a whim.
Do you remember that old, classic Twilight Zone episode where a little kid is a monster, because he's become omnipotent, he's a reality warper? The entire Earth has been "sent to the corn fields" and only that little neighborhood and it's few survivors exist, because the kid wills it? People live and die at his whim, and monstrosities are made for his amusement.
"That's a good thing, you did, Anthony."
That's the Scarlet Witch right now. But instead of being a spoiled brat who can be reasoned with, she is mentally and emotionally unstable. And before she causes any global harm that would be on a planetary scale, one of the logical options on the table should be to take her out.
As for the Cuckoos, there were viable options to neutralizing them. And they did not respresent the threat to all reality that Wanda did.