I just tested with
calibre's
ebook-meta command line program, and it did fine with unicode characters.
E.g., I put in:
ebook-meta Temp.pdf --title="ἀἐἠ"
And sure, enough, the title became ἀἐἠ.
Of course, you may have a problem if your shell/terminal/command line prompt doesn't support unicode input...
I imagine you could do it through calibre's GUI too, though for some reason, calibre's GUI confuses me more than using the command line does (and doesn't give me control over the file name and where it goes, which is frustrating)... so I prefer to use the command line tools.
Your mileage may vary.