But there is a solution!
This one eluded me (and google) for some time, but I am pleased to say that with the help of the Eclipse mailing list I have found the answer.
Open up the Eclipse preferences, choose Team -> SVN -> Console and uncheck the box that says ‘Limit Console Output’. With this option checked it seems that once Eclipse reaches the limit of the console output, it just freezes. I’m now able to check in a project with a lot of files and it’s all working excellently.