Sherlock was fulfilling his last (and first) vow to John and Mary. John and Mary would never be safe while the archive existed and Sherlock protected them. Normally, yes, I'd say this was an out of character, idiotic move, but apparently Sherlock honors his vows.

Was it made clear that she was there to kill him? I thought Mary was under the impression he had physical documents regarding her past and was there threatening him to get the documents and then kill him.

I don't think she did gain access. Perhaps she just gained information. I do think there's more to Janine than seen in this season. There's too many similarities to Moriarty and that weird mention of her by Magnussen. What did he have on her? I think they're setting up something.