That still remains to be seen at this point... though I'm still leaning toward her being "good" in her own way - she's trying to do something bigger than just take-out Volkoff, and has to stay in his graces.
I mean, she's obviously not outright "evil" - she saved Chuck and Sarah and completely hid all evidence of her two children from Volkoff (there's a huge plot hole on that point, but Chuck is full of plot holes).
The bigger question is what did she do to Chuck? She did it before Volkoff showed up, and he couldn't have ordered it since it wouldn't make sense to waste time doing that to someone that was going to eat it. Plus, she said Orion never wanted Chuck to see it.
An upgrade? The "true" Intersect? One that'd allow Chuck to permanently absorb the data?