AFAIK, .stl is inherently meant for triangulated geometry representation.
What you can do is to split rectangles into triangles - e.g. rectangle (n1, n2,n3,n4) gives two triangles - (n1,n2,n3) and (n3,n4,n1). Note that the order of n1,n2 etc is such that the normals obtained by cross product of vector, say n1_n2 x n2_n3 points outwards direction and there is consistency in this normal direction among all triagles. i.e. no sudden flips.