I think she knows what kind of monster Littlefinger really is, it was pretty apparent in her meeting with him earlier this season. Granted, she doesn't know the true depth of what he's done but she knows he's not to be trusted.
I'm thinking there's a chance he's the one being played this time. He's always ahead of the curve but I'm hoping this time he's the one who gets blindsided and by Sansa of all people.
Also, it wasn't just Littlefinger who threw the whole Game of Thrones into play. Varys also created instability by backing Viserys (and later Daenarys) pact with the Dothraki. It's not explicitly stated (in the show anyway) but it's entirely possible that Illyrio even received the dragon eggs to give to Daenarys from Varys.
That led to the initial conflict between Ned and Robert because Robert wanted Daenarys assassinated and Ned wouldn't do it. They patched things up from there but nevertheless Varys was working behind the scenes to undermine Robert.
Also, is it just me or are things looking really, really bad for the Lannisters now? I mean, be prepared for Cersei and Jamie to be dead next season at the latest, bad. If they make it through this High Sparrow business, they've still got a laundry list of enemies to deal with. There's the Starks who are now back in control of the North, there's Elaria Sand in control of House Martell now, you've got the joined armies of Daenarys and Yara Greyjoy, and their alliance with House Tyrell continues to deteriorate. They are basically against the whole kingdom at this point. Oh, and then there's those White Walkers...
Sansa know Littlefinger really wants her and she knows how to use it against him. How far she's going to take it remains to be seen as well. How much he gets played also remains to be seen.
Littlefinger and Varys were responsible for the whole goings-on since Day 1, though they were doing it from different angles to the same end. Varys is always working for "what's best for the realm", which in his mind wasn't Robert on the throne. Next best option would be putting Viserys or Daenerys on the throne, which is why he worked to get them safe into Essos via Illyrio's work. That's one thing that was excluded from the books was Tyrion's meeting with Ilyrio in Pentos and his way to Valyria. Gives some nice background on that part of the story.
I think Cersei has something she's working on with Qyburn as an alternate plan since she can't use trial by combat any longer. If next week's episode doesn't end up with
There's a LOT to try and work out by the end of the last episode and they're going to take 69 minutes to do it, since we have a super-supersized episode as a finale.