If you insist on working in indexed color mode, it is really impossible to avoid contaminating the color table with drawing colors. The secret is to work with color decomposition turned on. If you prefer to work with direct graphics commands (like TV and PLOT), I recommend you switch to Coyote Graphics commands. These commands are wrappers for direct graphics commands, but they have all the functionality and sophistication of the new function graphics system in IDL. With these commands you don't have to worry about what color mode you are in, etc. The commands will do the right thing for you. :-)
http://www.idlcoyote.com/.../coyote_graphics.php