There isn't much countering as in using a counter throw, as your opponent is already down in the ground.
Defensive measures are possible in some cases though. It depends a lot on how well the attack is performed though. I did randori with an 8. dan and he loved to use Sutemi Waza. When he went down, I flew no matter what I did. It would have counted as clean ippon each time. Theoretically I could have tried to prevent some of those "ippon", but it would have broken my arms. It was like black magic. When it happened all one concentrated on was proper ukemi, everything else would have been stupid.
When less skilled opponents try such techniques, they often telegraph them a lot more or are sloppy in their timing, use of angles, use of grips etc. So you may have the opportunity to drop your own mass down whilst staying on top. Then you proceed to pass their guard and take top control.
Against Soto Maki Komi and the like, it may be possible to push your opponent's shoulder with your free hand to pull your arm out of his grip.