Sorry, There is no direct way to remove the tool palette.
The "ToolPaletteManager.Remove" method does not work and we have already logged this.
As a workaround, you may consider removing the catalog item from the .atc file since it is an XML file and can therefore be parsed / modified by your application but is not recommended.
ToolPaletteManager class was moved from acmgd.dll to AcTcMgd.dll in AutoCAD 2013 with some new classes and methods updated. But the API for tool palette is not comprehensive with many missing features. It should have some easy generic methods like Create(), Remove(), Load(), Unload() for tool palettes.