Well, there are a few options, but, depending on the situation, code isn't the easiest way that I know to deal with this particular circumstance.
First, if your plug-in has a particular capability that is required for accessing those options, you can ensure that your users do not have that capability and write a check in your functions.php to see if user->has_cap(). It really depends on what plug-in you are using and how it's set up as to the best way to incorporate this.
Another option, if it has capabilities would be to use something like the Role Scoper Plug-in or the Members Plug-in to remove that capability through a User Interface instead of code.
Another option, if your plug-in doesn't have specific capabilities would be to set the user level to something like Editor and then use the Admin Menu Editor Plug-in to remove the settings from that user-level's admin menu.
Personally, I'd recommend the Admin Menu Editor, I use it on most of our projects to limit the user's access to various things that I don't want them to accidentally break.
I know it wasn't exactly the answer you were looking for, but if you provide some more info on that plug-in, specifically a name and a link, perhaps I can check into the best way to hook into it.
Hope this helped a little.