Figured it out by looking at other scripts, turns out all you have to do is insert this when you want the item gone
%currSlot = %obj.currTool;
%obj.tool[%currSlot] = 0;
%obj.weaponCount--;
messageClient(%obj.client,'MsgItemPickup','',%currSlot,0);
serverCmdUnUseTool(%obj.client);
%obj.unMountImage(%slot);