なのに、ああいうことになったんだ。敵さんの意図も正体も分からない以上、こっちもそれなりの体制で現場に臨むべきなんじゃねえのか」
After a recent failed mission, the characters are discussing that for the next missions, they should be careful and watch out for their partners. Then a character adds this.
The first part is akin to "Given we don't know the enemies' intention and their true nature"
I understand he's saying it like... we should be careful or whatever but I'm a bit stumbled on the nuance of それなりの体制で. I assume で is "by the way of" nuance.