Can one cast a spell-like ability such as Touch of Darkness, hold the charge, then move into melee range and make a touch attack with that ability thus preventing an AOO?
I believe so, yes, as spell-like abilities follow the rules for spells except as changed by the spell-like ability rules (that say nothing about changing that).
Additionally I don't think you have to hold the charge at all. Unless I am mistaken, you can always move between taking the action to cast a spell and delivering the free touch it grants. Could be a 3.5 thing that didn't port over.