Why don't you embed a libavogadro-based widget which would draw the created molecule (after exporting to CML or a similar format) in 3D.
libavogadro is currently being polished so that Kalzium can use it from KDE 4.0 on as the 3D engine for drawing 3D-molecules.
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The idea of a 3D view is quite cool and libavogadro seems to provide just that. I'll do some experimenting and perhaps it will be ready for Lithium. Thanks for the suggestion.