How do I stop tools from automatically activating?

That is to say, whenever I click on a tool like Scale or Translate, it automatically keys into my mouse and will do it’s thing before I even click the object or face I want to work with, which makes editing meshes a bit tricky. Problem is, I can’t find any option under preferences to stop this from happening, so what am I missing?

You select what you want to change followed by the tool, not select the tool followed by what you want the tool to change http://www.blender.org/manual/modeling/meshes/editing/basics/translation,_rotation,_scale.html

Also easier to use the keyboard shortcuts, G = Grab, S = Scale, R = Rotate

So then…Let me get this straight, we’re expected to treat the tools like cursor modifiers, not like…Point and Click tools?

yes. You select what you wish to manipulate first.,… and then use the tool…

it may seem counter intuitive, but it’s really the best way when you get used to it
and as richard stated… the keyboard shortcuts make this a 1 click action…~

“click object, hit s , move mouse, click to finalize”, for example, is much simpler than;
“select tool, select object, move mouse, click to finalize” (its still a 4 step process, but because the shortcuts are always under the left hand (or should be) it becomes very fast when you “muscle memorize it”)