As far as I am aware, Construct 2 correctly handles unicode. It exports everything including the Javascript contents and filenames in UTF-8. Perhaps there is a server configuration issue that is causing a problem; if the server is trying to use a different codepage, it might corrupt the file contents or fail to locate files. It's hard to comment further without an up-to-date example.
I'm also not sure if we can automatically rename files without possibly causing naming conflicts. I also don't want to make Construct 2 rename things if the problem is just with the server.