I think you can configure Konqueror to automatically reject Javascript from individual/specific sites, so that it won't ask you again and again for confirmation. It's in Settings > Configure Konqueror > Java & Javascript > Javascript tab > Domain-specific group > add a New rule (automatically accept or reject, etc)
As for toolbars, I'm not so sure. But I think you can prevent toolbars from being edited (through Configure Toolbar), but I think they can still be moved. To prevent a certain toolbar in Konqueror from being edited, go to ~/.kde/share/apps/konqueror and open up konqueror.rc. Look for the ToolBar line of the toolbar you want to "lock". For example, if I want to prevent the Location Bar from being edited, I look for this line:
<ToolBar newline="true" noMerge="1" name="locationToolBar" fullWidth="true">
On that line, I add a noEdit="true" entry, so that it would look like this:
<ToolBar newline="true" noMerge="1" name="locationToolBar" fullWidth="true" noEdit="true">
Then save the file. At least, that's how I did it on my system. I'm not sure if it's the correct way or if there's an easier way.