Legion-7's decision for them to run was a smart move. There was just so much they didn't know and too much danger.
They don't know how Green Vine is able to infiltrate them even though she should be too weak to do so. It could be because of the incomplete universal artifact in her possession or the fact that she had the help of the first sage.
They were not sure of what she was capable of, and they didn't want to find out by using brute force. Besides, she could easily escape into another vessel even if she had failed her attempt to infiltrate them. She was just too dangerous back then.
But things have changed now. Green Vine has been captured, and the strange creatures have been cut off from the first sage. This means they can do anything they want to them.