Yes, you can mess up your faction even with illusions. Think of them as just a change of race. Everything you have done still counts but is now viewed through the lens of that different race. A prime example of this is using the iksar illusion. They are all worshipers of Cazic-Thule, so an agnostic iksar or one with a different religion is still anathema to them and requires faction work to be accepted.
The short of it is, if you want to be accepted in Neriak, don't kill the guards. The illusion will only give you as much protection as a turncoat dark elf would receive.
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