I suggest a bigger X, and possibly a tooltip explaining that it was excluded. Many, many users here don't notice the X until it is pointed out to them. IntelliJ projects depend heavily on exclusion lists due to the way our build system works, so users commonly have excluded files without realizing it.
(The "file is excluded" inspection was great too, I was sad to see it go during 7.x EAP.)
A custom scope would be one solution, although that probably would be too "heavyweight" for a relatively rarely used feature.
Perhaps the scope could only be made available if anything is actually excluded? Just an idea...