You don't keep them from acting by using command, you simply dictate what one of their actions will be, if they fail a save. The rest of what they do on their turn is still up to them. They can yell for help, a free action that counts as acting. They can draw a weapon as you force them to advance, an action. Command is a first level spell for a reason, it's not THAT powerful.

Also, the undead domain ability lets you get healed by negative energy, but it doesn't say that it makes you look dead in the slightest. Pretending for a moment that it DID make you actually look dead, it still only lasts for 1 round per caster level, so about six seconds. That wouldn't be long enough to get their guard down and get them in there with you.

EDIT:
Also, I'd actually consider being manipulated by a spell like that to count as taking an action during combat. The idea of the flat-footed mechanic is that you get the drop on someone, that they didn't expect something to happen. Think of what the term "being caught flat-footed" means. If you found yourself being forced to march towards a malevolent spellcaster, you wouldn't be flat footed for very long- certainly not long enough to end up in the same cell as him and allowing him to strangle you.