I think for Skylar it began with cooking Ted's books because she wanted to help out someone she had sympathy for (and maybe was attracted to him). We all make mistakes and i'm pretty sure some of us made also some illegal ones that we consider minor like fudging taxes and such but in the end they are still illegal and carry penalties if caught.
Now cooking a companies books is no shaving off a few hundred bucks off the IRS, this is something people go to prison for and Skylar made that decision all by herself because she thought that having a steady, well paying job in their circumstances (Walt assembling a huge medical bill with a comparable small income) would be better than no job so she "got over herself" in the same matter as Walt.. a small, seemingly innocent skip over the line with the full intention of going back once matters have settled down.
Both plans got shot when outside interference scrambled their plans (as it always happens) but instead of owning up and putting an end to it with all the consequences both have dug themselves ever deeper, admittedly Walt's path has been much darker and more violent.
Now with this episode she has crossed the final line by urging Walter to "deal" with the problem and we all knew what she really meant. It's been a while coming since Skylar fully embraced Walt's actions and has been actively helping him but this was the final straw, now her hands are truly dirty and she can't pretend to be a white collar criminal anymore.
This is why i love this show so much.. every action has consequences and you can't escape them.