You can safely SV an S Tandem Top. If she sets a meaty HS TT and your SV whiffs or gets blocked, the hitstop is nowhere near enough to get you through the disc, and you'll get counter-hit into a free combo.
Blocking in the oki situation (and don't try pulling the "you shouldn't be in that situation", since a simple 2D by itself leads to that) is far and away your best option. Millia DOES have reversal safe oki, and frankly it's not terribly difficult to do. I know you'd hate to do this, but just block her mixup. The matchup for her against OS is already in your favor. Instead of risking a CH and a reset into the same damn situation again, you can block and get away and proceed to rape her in the neutral game and get your offense.