Tunnelblick is intolerant of files that are not required by the VPN or that it doesn't know how to secure; a .csr file is both. I am hesitant to start accepting .csr files (or any other file), which would complicate both the code and the documentation without a good reason.
The usual solution to problems like forgetting to delete a file is to use a script to automate the procedure. And in your case, in which Tunnelblick provides a reasonably clear message about what the problem is, and the problem is so easy to fix, I don't see a good reason.
But if a lot of other folks respond that they also have this problem, I'll reconsider.