Yes, you definitely can. 2D Toolkit helps improve the 2D 'workflow', and provides some specialized components that make it easy to get to get sprites into your game and into your scene. It's good at managing sprites, putting together animations, etc... 2D Toolkit doesn't care if your game is side-scrolling, top-down, or whatever.
That said, the hard part is still going to be scripting and the Unity environment itself. You need to have a solid grasp of Unity and scripting in general, to get a lot of value out of 2D Toolkit. If you fully understand Prefabs, components, GameObjects, transforms and how to code, you'll have a great time. If not, 2D Toolkit won't be of much help.
That said, I don't think I could do 2D in Unity at all, without 2D Toolkit (or a competing 2D package).