A scalar can have a sign, just not a direction.
You actually clarified everything right there. Under that definition, work is a scalar with a domain from + to - infinity. Energy has a domain of 0 - +infinity. The definition of a scalar I was using in my AP physics class was that a scalar had domain 0 to +infinity, and everything else was a vector, because everything else would constitute a direction. Under this definition, which would appear to be the prevailing one, then work is a scalar. It just has a +/- sign where energy does not.
I went through the http://asd20.org/education/components/docmgr/default.php?sectiondetailid=37896&fileitem=43607&catfilter=5055" again, and the instructor specifically states that the answer is a scalar because the dot product can be simplified as [scalar * scalar * cos direction = scalar].
Generally speaking, I think my logic for coming to the conclusion I did is straightforward though: "A vector is any quantity that has direction"; few people would disagree with that statement, though apparently it isn't quite right. "magnitude is the same as the absolute value." In other words, the magnitude does not include a +/-. We use the same symbolism for the two operations. --> "Anything where |V| != V is a vector" --> "|cos pi| != cos pi." --> "Work is not a scalar, it must be a vector".
If all of those statements hold, then the logic is sound, so somewhere in there a distinction must be made that makes a quantity with 1 dimension of direction a scalar. In the end, I guess it makes sense though. You can't really consider a number line as having a direction, as there are only two choices of angle, 0 and pi. A plane has one choice of direction, that is, an angle that can take on any (real) value. A 3D coordinate system has 2 free directions along which we must define an angle. Thus a better way to define a scalar is by the number of free axises of direction it has. A vector is any value more than 0, a scalar has 0.
Curiously, we end up then with two classes of scalars, those that must be 0 or above, and those that can take on any real value. Temperature, Energy, Counts, Speed and some others fall into this first category. Things like Work, Rates of changes of the first class, and some others fall into this second class. So I guess my misconception was to group this second class in with vectors when it's really just another type of scalar.