Should I let my wife put our daughter in her Russian passport?

I don't think you should be worried about the passport thing. Especially if your daughter is an American citizen. What you should consider is how much you trust your wife about letting your daughter go with her, while you stay behind. If that's okay, then no worries!

I've done this before when traveling to Bulgaria with my son.He is Canadian and was a pain to get his passport out.Just tell her to make sure she takes your daughter birth certificate showing the parents names in case of emergency.That way she can ask the Americans embassy for help.You might also want to check if Russia requires letter from the father allowing the child to travel.A lot of countries start asking for such a document in the last year

There probably isn't anything to be worried about unless the Russians get totally pissed off at us again and then take it out on regular folks. And things at present look headed that way.

What I'd be most concerned about is whether or not the Russians consider your daughter to be a Russian citizen. THAT would be your real exposure - for both your daughter and your wife.

Best check with USA immigration as your daughter might need a USA passport as returning might be an issue>Your wife is looking for issues best get this cleared before they leave>Or try to>?

Yes. Be very worried that she will take your child to Russia and not come back.