Euphemia in the sickbay did not say things like: "Black tools very faster red bucket." or "sail to sky cloud loudness." All of her sentences were grammatically correct and understandable. And she did not ask Suzaku to eat only green-skinned children, not purple-skinned children, in the future. She didn't ask Suzaku to shoot a green flying shark. She didn't ask Suzaku if she had done well at dueling the ambassador from Mars, or at solving a crossword puzzle tattooed on the side of a six-legged elephant. Euphemia talked about matters which made sense in the situation.
Her mental and physical condition in the sickbay was not bad enough to prevent her from giving orders to kill that might be obeyed. How could Euphemia or the geass command simply assume that the odds that an order to kill from her would be obeyed were so low, (ten percent?, one percent?, 0.1 percent?) that it wasn't even worth trying? No matter how low the geass command estimated the odds, it would have to make Euphie try it. Unless the geass command believed that trying to make Euphemia physically kill Suzaku had a better chance of success, which might be ruined by trying to to give an order which might warn him. But the geass command did not make her try to kill Suzaku physically, Anyway, success in killing Suzaku would not be nearly as lethal as success in ordering the Avalon to attack at least one Japanese ghetto.
The geass command didn't make Euphie give a command to kill, therefore it never gained sufficient control of her to make her do anything. Therefore Euphemia defeated the attempt by her geass command to regain control in the sickbay. And very rapidly too. Her defeat of the geass command in the sickbay (and thus Suzaku's survival) only makes sense if she defeated the geass command before and thus knew exactly what to do to defeat it within seconds of becoming aware of it trying to take control again.
It seems silly to suggest that Nunnally did not defeat her geass command in an attempt to make it seem less possible that Euphemia defeated her geass command.
Euphemia was conscious and could talk rationally after the geass command tried to make her kill. But she did not try to order anyone to kill Suzaku or any other Japanese person. Therefore she was free of the geass command while still strong enough to kill. Therefore the geass command did not give up trying to make her kill because it found that she was too weak. Therefore the geass command was defeated by Euphemia. I think that is very strong and very convincing logic.
Show me a logical sequence of events, each with at least a fifty percent probability of resulting from the previous one, which would have led from taking Euphie hostage to a worse result for the Japanese cause than the failure of the Black Rebellion as shown in the series?
If your proposed chain of events has two links each with a 50 % chance of following from the previous event, the end result will have only a 25 % chance of resulting from taking Euphie hostage. If it has three links with a 50% chance of resulting from the previous event, the end result will have a 12.5 % chance of resulting from taking Euphie hostage. If it has four links each with a fifty percent chance of resulting from the previous event the end result will have a 6.25 % chance of resulting from taking Euphie hostage. For your argument to be convincing you will have to have few links in your chain of events and prove that each of them has a very high probability of resulting from the previous event. Otherwise your predicted disaster will be only one of many possible results.
Why do you assume that making Euphie a hostage or simply a prisoner would require that Lelouch explain to the world that she was insane, or possessed, or bewitched, or under some kind of mind control? Why do you assume that explaining to the world that Euphemia was insane, or possessed, or bewitched, or under some kind of mind control would require revealing the truth about Lelouch's geass power?