I was trying the last EAP build (5368) and now GWT plugin recognizes the toolkit under linux but there's another bug, when trying to run/debug a GWT configuration appears an error message which says "......../java.exe not found".
I could fix this by modifying com.intellij.gwt.make.GwtCompiler line 169, changing the original by:
command.add(projectJdk.getBinPath() + File.separator + (SystemInfo.isWindows ? "java.exe" : "java"));
Unfortunately this plugins uses some features which are not part of the open API so it is a little tricky to compile.