Yeah, it get’s a little messy. OK, a lot messy, but it can be done. I added three extra Properties to a rectangle, Color1, Color2, and Style. This way you can pick both colors of the gradient via scripting.
if event.propertyName=="Color1":
from java.awt import Color
from java.awt import GradientPaint
o=event.source
x1=o.relX
y1=o.relY
Color1=o.Color1
x2=x1+o.relWidth
y2=y1
Color2=o.Color2
o.setFillPaint(GradientPaint(x1,y1,Color1,x2,y2,Color2,1))
When changing the gradient this way, the Fill Paint type becomes unknown, so you have to change it to something it recognizes before yo can do anything further to it. Like copy/paste, or adjust your styles:
Perhaps someone else can chime in and tell me what I’m missing… 
Here’s a window to look at.
AnimatedGradient_2014-11-25_0850.proj (6.97 KB)