I came across this article when I was pondering teaching the FTA to my multi-variable calculus class. In the end, I didn't have time to include it. It is nice in that it relies only on Green's theorem which we get through in the first semester. On the other hand, it is clear that they are largely being clever at avoiding introducing new definitions or standard theorems (for instance they use Cauchy-Riemann equations for polynomials without really saying so). I think it's nice nevertheless.
http://www.math.binghamton.edu/paul/papers/LoyaFundThmAlg.pdf