(defn r-squared [x y]
  (+ (* (- 0.5 x) (- 0.5 x))
     (* (- 0.5 y) (- 0.5 y))))

This may not be right, but it's closer to what you probably meant.

(defn calculate-pi [throws]
  (loop [hits 0
         throws-left throws]            ; initial number of throws
    (cond
     (zero? throws-left) (* 4.0 (/ hits throws)) ; all thrown, return value
     (<= (r-squared (rand) (rand)) 0.25) (recur (inc hits) (dec throws-left))
     :else (recur hits (dec throws-left))))))