If you rig your line so that you can unclip it you won't have to worry so much about shooting down the middle of a fish. I did this once and you're right, it's dead hard getting your spear out. Landed on some rocks untied the line and pulled it right through in the end and had to re-tie. Took ages.
Now I use a quick release catch thingy so I can unclip, pull the line through the fish (if required) and quickly re-attach line to the gun.
I use to have a clip on my rob allen but since adding a reel to it i couldn't really use the clip which was on it. I am trying to sort out a new clip though so i can unclip my line again.