You can move the dock's location and size by going to System Preferences > Dock. Rather than keeping the dock at the bottom, where the mouse needs to be often, move it to either the right or left sides of the screen.
I auto-hide the dock on the left side of the screen (I'm on a 13" MacBook Air, so my vertical space is limited too). You could also use @VxJasonxV's suggestion of removing the apps from the dock. Most of the programs I launch are via spotlight (the ⌘+Space shortcut is very useful). And the last trick I use is BetterTouchTool. I bound five-finger-click to ⌘+Q, which makes it very easy to quit applications, but not so easy that it accidentally quits applications I didn't mean to quit.