I don't know enough about Eclipse RAP/RCP to provide a definitive answer, but as long as you can follow the portal spec for the apps you develop, it might work. Following the spec means that you have to develop portlets rather than servlets, and all communication to the server (from your AJAX or rich client code) must use the portal URLs.

One other concern I have is whether RAP or RCP client code will play nicely with the portal UI - after all with a portal no individual portlet has control over the UI because the portal enables multiple portlets to be displayed on a single web page. RAP should fit into that framework OK (see the portal forum for the various discussion of AJAX use in portlets). But I am not sure if RCP would fit since that seems geared towards a stand-alone client.

Finally, the Eclipse RAP/RCP tools are probably geared towards stand-alone use (that is, not within a portal). Thus you will probably find yourself fighting the tool (Eclipse) and the code it creates. You might be better off developing portlet code with AJAX capabilities.