Not to defend anything that's currently going on, but you have to consider the possibility of a dispute at the border over whether someone is a citizen or not.
Honestly, this is why I don't complain very much about biometrics and databases, because the realistic alternative (potentially being detained at the border while they try to guess whether your passport is forged/altered/stolen) is much worse.
I can't remember the name off the top of my head but I recall a famous "no fly list" story about someone who was prohibited from returning to the US because their name was a potential misspelling of a suspected terrorist's name.
I, too, remember this happening and being reported, maybe the NYTimes.
I'm having trouble finding dates for some of these cases and none seem to have happened while GWB was POTUS. But here are a few links involving US citizens whose ability to travel into and out of the US were curtailed. None of the following links are the case I remember, which involved an American who was a father (from NY?) and who had been stranded from his family in the US.
• U.S. Veterans Stranded Overseas|Challenge No-Fly ‘Terror’ List [0]
• ACLU challenges constitutionality of no-fly list [1]
• No-fly list grounds another San Diegan [2]
• How a Young American Escaped the No-Fly List [3]
I hate to be obtuse, but this is much more comprehensive. A "no fly list" at least gives you the option of traveling by sea, or flying into Canada or Mexico and coming in through the border. Horribly inconvenient, but not a blanket ban.
If you have thousands of dollars and a week or two to waste.
> Canada or Mexico
If you can get a visa for those places. Both of your ideas are things I, as an affluent Westerner, would try if the US government stuck me on a no-fly list, but for the people targeted they may simply not be possible.