As you state, we are limited in what we can do. However, one thing Obama could do is to tell his staff to quit referencing transition every third word.
I also think Presidents can talk about these matters in general terms that help to remind foreign nationals that things don’t always turn out rosey when governments are toppled. He can also state that we ultimately wish the best for the Egyptian people, but that he doesn’t think what is taking place right now is the best way to achieve that. He could also point out other nations where regime change took place that turned put badly.
Other than that you stay in close contact with Mubarak expressing concern. You do not simply jettison an old friend to the U.S.
Then you contact others leaders in the region and keep abreast of what is going on there.
I would also try to develop some back channel contacts that might be able to help defuse this situation if at all possible.