Due to a bug in a Companions quest, I had to use the console to skip over one quest (see bug and comsole solution at http://elderscrolls.wikia.com/wiki/Blood%27s_Honor). Unfortunately, this leaves a number of NPC's in scripted positions. This includes the guy who mans the counter at Warmaden's. Is there anyway to reset the AI of these characters so they start going about their daily lives again?

I see there is the Tai command, which turns NPC AI on and off. I have little experience using the console. Will trying this affect other active or future quests? Will it affect old saves when I reload them?

Tai isn't going to do anything useful in this case.
You can click on an actor in console mode and type 'ResetAI' to make them reevaluate their AI packages, but if there is a script that is controlling a package and the variable is still set, they will revert to what they were doing anyway.

So these poor NPC are going to be stuck where they are for the rest of time?