Sorry about the delay in reply, I've been away for a while.
I'm really sorry to hear about the Vita getting updated. The app just adds rows into the video database and I can't see how it would mess up memory cards let alone breaking HENkaku etc and forcing you to update. Only thing I can think of is that the 0.8 release did more than necessary access to the database, which was fixed in 0.9.
If anyone else gets problems with the video or music app, you can try first pressing triangle to empty the database, if that doesn't help, reboot and select "rebuild database" from the safe mode menu, that will rebuild the databases using the Sony app or format the memory card.
Just to give a bit more info, the app adds data to the ux0:mms/video/AVContent.db and ux0:mms/music/AVContent.db files, so a memory card format completely removes any effect this app can have on your system.
If you get a corrupt database somehow, copy these files and make a github issue and I can try to debug, then rebuild database or format the memory card.