There is nothing wrong with checking in .project and .classpath. I would do so, if your build.xml isn’t able to create both of the files for you. As you said, it’s uncomfortable to miss these files when you try to create a new eclipse workspace.
Before you check in .classpath you should be sure that there is no absolute path in it. Convert it into a relative one with a text editor.
Edit: Or even better, use eclipse classpath variables in your otherwise absolute pathes, like @taylor-leese commented.