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There's no way to do this now, but I think it's a good idea. A work-around, obviously, would be to actually change site-packages files on disk to be read-only, but that very possibly will break package management. I don't know why Python package managers tend to leave installed files writable since that does set people up for this problem and defeats the advantage of supposedly working with a known set/version of packages.
If you right-click on the notebook tabs and select Hide Notebook Tabs you will get a popup menu instead of tabs and that does put a star icon next to files that are in the project, which maybe would also help a bit with this.
We'll try to address this better somehow, probably by warning immediately when a non-project file is edited and adding a way to disable that for the one file or all files. The issue with this is likely going to be that lots of people don't add their source files to the project, but failing to do that can defeat some of Wing's features anyway so it may not be a bad thing to warn about it.
Thanks for the suggestion!