The T-X still wants to try and corrupt that potentially vulnerable AI system with her sexy drill-finger and stuff, so as to remotely control... And if that's not possible, will see it as a possible threat to an eventual Skynet.

Which could possibly over-ride the 'kill John Connor' thing, in terms of priorities.

However! There are what looks like a bitchload of other characters already involved and more could be complicated! I'm willing to have her silently sit stuff out!