I would advise you to do the update by the server itself. When I had problems updating (my server provider is very limited) I downloaded the latest version of woocommerce to my computer and then uploaded directly to the server (you could use some FTP like Filezilla). To the plugins folder (something like public_html/wp-content/plugins). You should delete the older woocommerce plugin folder before uploading the new one.
It has worked for me, but maybe your problem lies on some update conflict, I don’t know since my error was different.
This is a made up solution from a newbie, but if you do it right and do a backup before trying it, I don’t think it would harm in any way.
Good luck!
