If you are just doing 2D work, don't create a 3D drawing. In your part, go into sketch edit mode, hit CTRL-A to select all and copy that to the clipboard. In Alibre open a new drawing, not a part, a drawing, go into sketch mode, select everything and delete it (the drawing borders, title block, etc). Paste the stuff in the clipboard and export the drawing as a DXF file. Import that into SprutCAM and and create your holes off of that.
I also got stuck in the "everything should be in 3D" train of thought. If it's 2D or 2.5D just stick with a flat line drawing and set your depth in the parameters window.