Yeah, Sansa's story is still on track. The only real change there is they offered her Loras(which she's going to be even more salt about not getting to marry than Willas
).
Ser Dontos seems to have been written out, but that's no biggie.
Any time spent with Varys is time well spent IMO. His character and the actor are both great. Consider it filling time with actors that will be on the payroll for seasons to come while they chop lesser characters that they're unwilling to spend time and money on casting.
And look at this Sansa/Littlefinger/Varys arc from a non-readers POV. They still have no idea where this will end up going, so in that they are successful.