Done!
After the line ~ 465 in jqplot.barRenderer.js:
this._dataColors.push(clr);
.. add the following code:
var grd = ctx.createLinearGradient(points[0][0], points[0][1], points[1][0], points[1][1]);
// dark blue
grd.addColorStop(0, '#02618D');
// light blue
grd.addColorStop(1, '#008ACA');
ctx.fillStyle = grd;
opts.fillStyle = grd;
This generates de gradient object capturing the bar coordinates and adding it to the options parameter.
Not sure if this will do any conflict. In my case works fine :)