The Skulls can be avoided in their first appearance (Resucing Miller / Phantom Limbs) with a little bit of patience.
First, use your IntScan to mark all 4 Skulls -- two at the top of the bridge, and 2 along the slope to the left of it.
Now, you wait. The skulls will slowly shamble forwards, with the left skulls going down the slope, and the right skulls approaching and then beginning to go down the slope on the far side of the bridge. Your approach should be straight across. Once the right-pair has started down the slope, make your move. You have a rather narrow window where the Right skulls are far enough down the slope to break line of sight before they come back up the hill and camp the edge of the bridge.
Once you're a good 100m on the far side of the skulls, feel free to whistle up D-Horse, fling Miller over his back, and casually ride the rest of the way to the extraction site.
Alternatively, change the helicopter's landing zone. If you take out the radar dish, you can have your chopper land right outside the prison. (Just make sure the guards are unavailable/incapacitated!)