Lisa, confusing? All right, let's see if I can't break down the reasoning for her actions with a little logic.
As you may or may not know, it has been confirmed in the first DOAX that Tina and Lisa were childhood friends before pursuing their careers. That should indicate Lisa has a good soul after spending so much time with such a cheerful person. However, she always had a thing for science. If anything, she's torn between her dream as a scientist while also still remaining relevant to Tina as a childhood friend. In order to pursue both, she had to get involved in the inner workings of what was the former DOATEC, unbeknownst to her the eventual corruption that divided it... all while working under the branch of the DWA sponsored by the same company under the persona of La Mariposa to relate to the dream of her closest friend.
In DOA4 she had a clear conscience that Donovan was going too far with the Alpha project, but for the sake of pursuing her career in science, she had to keep working behind the scenes and put up the charade until the time was right (after all, if she blatantly rebelled against Donovan, she'd be assassinated). And knowing her dual-personality on and off stage, charades are nothing to her.
Given these circumstances, her actions are justified. After all, would you as a notable top scientist leave a project associated with a madman with his own military, a top assassin (or assassins?), and ninjas who will use any means necessary to hunt him down including killing those involved at the drop of a hat? I don't think so... you'd keep it cool, act behind the scenes, and wait for the safest opportunity possible while still making that dough. By that logic, Lisa is doing the smartest thing she can do, while not completely drawing the ire of the Mugen Tenshin's wrath, let alone Hayabusa.