You are not allowed to embed yEd in Eclipse as a plug-in or as part of a plug-in, see yEd Software License Agreement section 1. LICENSE CONDITIONS:
The Licensee is granted a [...] right to install one copy of the Software and use it as an application.
If you want to build an Eclipse RCP plug-in that requires graph drawing capabilities, you will need to use the yFiles diagramming library. yEd is built upon this library as well. yFiles is available for several platforms (.NET Forms, .NET WPF, JavaScript, JavaFX, Swing). For Eclipse RCP, yFiles for JavaFX is the right choice.