With Ada, I get the impression she is working for some "greater good", with her rationalizing her involvment away as a nessesary evil. She acts bothered at the loss of innocent life, and in RE6 even goes out of her way to save civilians. She also regrets having to retrieve the G-Virus in Death's Door.
Her sometimes cruel and uncaring attitude is a front, as seen in her RE3 epilogue. So while her actions are sometimes malevolent, it seems pretty clear her intentions are not.
That being said, I'm not sure CAPCOM have actually figured out what her ultimate goal really is, considering the weird direction they considering taking her in RE6. Hopefully they figure it out at some point. For all we know, her true organisation could be the Connections, or the Chinese Shen Yai.