I have the same problem.
After some tries I found this solution
create a just empty module named java-dep-python etc then add it to project
<module relativePaths="false" type="JAVA_MODULE" version="4">
<component name="NewModuleRootManager" inherit-compiler-output="true">
<orderEntry type="jdk" jdkName="Python 2.7" jdkType="Python SDK" />
<orderEntry type="sourceFolder" forTests="false" />
</component>
</module>
change all your mixed modules to add this new empty module as dependency
<module relativePaths="true" type="JAVA_MODULE" version="4">
<component name="FacetManager">
<facet type="Python" name="Python">
<configuration sdkName="Python 2.7" />
</facet>
</component>
<component name="NewModuleRootManager" inherit-compiler-output="true">
... ...
<orderEntry type="inheritedJdk" />
<orderEntry type="module" module-name="java-dep-python" scope="PROVIDED" />
... ...
</component>
</module>
Note that the PROVIDED keyword do help that this module is not required by any artifacts
It works for me, now that standard python imports are good.
IDEA 14.0.3 build #IU-139.1117