Don't you end up duplicating every line break that way? I think it should be

    perl -p -e 's/\r//g' Bad_Microsoft.csv Good_unix.csv

After all, Microsoft files usually end in a carriage return followed by a line break and not a bare carriage return, don't they?

Not really or at least I haven't had that problem. It would be a problem if they used both \r and \n at the same time. in that case you can always do \r\n to \n or something like that.