I was able to get around this problem by using ScalaProject.scalaClasspath.fullClasspath instead. It causes the compilation to fail for non-Juno profiles, so the proper fix requires merging the pull request you've mentioned. It was good enough for my current purpose though.
After that change I was able to build the plugin (all integration tests passed OK). I've installed from the generated local update site it with a minor issue - I had to disable "Contact all update sites ..." checkbox in the Install new software dialog, because otherwise I got a dependency resolution error claiming that org.scala-ide.scalatest 0.9.1 requires JDT [3.6.0,3.7.10) even though I've set it to [3.6.0,4.2.10). Apparently the P2 got confused because I had the same version of the plugin available in my local site and remote scala-ide ecosystem update site.
Now the good news: I was able to run a few test I have in my toy projects (I'm just learning Scala right now) using ScalaTest plugin and it worked smoothly. Run As > ScalaTest showed up in the right places, and Package / Suite / File / Test modes worked as expected.
Would you like a pull request that expands JDT depedency range and adds scala-ide-juno-master-scala-2.9 profile?
cheers,
Rafał