If you're planning on setting 'em flush in the metal, you could drill through the pearl and set a rivet there, and then set the stone flush in the head of the rivet. It might help to ask your friendly neighborhood jeweler or someone who's done something like that before, or you could try your hand at setting them yourself. <a href="http://ganoksin.com/borisat/nenam/gypsy-setting.htm">This</a> page from the ganoksin project's website has some basic info on flush setting. The Orchid forum at ganoksin.com is a great place to meet with jewelers and decorative metalworking enthusiasts of all stripes.
<p>I reckon there are a number of creative ways you could work gems into your handle. If the stone is big enough, you could build a backed bezel and rivet that into an inset on your pearl handle, then set the stone in the bezel.
Hope this helps,
Guido Reichstadter