I don't think you'll need to build up the floor to clear the water pipe.
1) Measure the distance from the top of the existing concrete floor to the top of the water line + 1/4".
2) Buy a 72" long section of squared-off 4" wide, "U"-shaped angle iron - which will be cut in half (36" each), with one half placed (front-to-back) on each side of the safe cavity.
3) Cut the sidewalls of the angle iron so that the 4" wide top flat towers 1/4" above the height of the water pipe.
(Notches for the waterpipe would need to be cut into the angle irons in order so they can straddle the waterpipe.)
4) Use plastic sliders and a couple of beer-crazed friends/relatives to tip the back or the (empty) safe on to the angle irons (now converted to a pair of rails) & slide that puppy home.