Are you sure you want to get a histogram with >60000 bars? Even with one-pixel wide bars this would fill a very big space.
As far as I understand, the number of actually drawn histogram bars is determined by the histogram_bins option, not by the number of input values.
That said, I agree that GD::Graph has some severe limitations (like the inability to do subpixel rendering), and should usually only be used for quick-and-dirty solutions, or when no high quality solution is available.
Apart from gnuplot there's also Chart::Clicker, which I haven't used yet, but I've heard many people speak well of it.
- links to (nearly) everything that is Perl 6.