Javascript is processed linearly, so the more data loaded, the longer it takes. I would suggest a load on demand type of charting, showing only a part of the data at any one time.
Otherwise i would suggest moving to Flash / Silverlight (if you are developing in .NET)
Edit
Visifire for Silverlight. it is open source and can be found at http://visifire.com/.
Also, MS just released the MS Chart Controls (http://code.msdn.microsoft.com/mschart), which need .NET FrameWork 3.5 SP1, these can be used natively in WinForms / ASP.NET (server rendered, using ASP.NET AJAX load on demand would be a easy).
FusionCharts is free for Flash: http://www.fusioncharts.com/free/