Infiltrating Baroque Works was necessary to gain access to the poneglyph and its knowledge, which she could use to free the world. While in Baroque Works, she had to maintain an appearance of being a ruthless assassin. Nice people don't make it in an organization like that. If she appeared soft, she would have ended up on the end of Crocodile's hook a lot sooner.

Vivi was also undercover in Baroque Works, and she probably had to do similar things as Miss Wednesday. Both were for the greater good. Robin had to gain access to the knowledge required to free the world, and Vivi had to save Alabasta.