The question keeps coming up, does the dominated person know the spell is harmless when it begins affecting them. The answer has to be "Yes!", otherwise the harmless tag has almost no meaning. Per the description of harmless, it's an act of will to make a saving throw against a harmless spell ("if they choose to"). Implicitly, there must be knowledge in order to make a decision.
I do think that the target of the spell must identify it via Spellcraft as harmless (or be convinced via roleplay or bluff/diplomacy) in order to avoid requiring a touch attack with the spell.
A lot depends on how you imagine the "fluff" of dominate person. I'm picturing a subject that hasn't had his attitudes and allegiances altered, he just suffers from a compulsion to obey very specific sets of orders. Like a genie, he could look for loopholes in the wording of his commands.
I finally got around to hitting FAQ.
Is it a stretch to say that upon being dominated, your perception of who your allies are immediately changes to be identical to that of the casters? If so, I would say you would definitely make a save against any spell cast by an opponent (your former allies).
Further, I guess I'd also say you don't know if a spell is harmless or not, unless you succeed at an appropriate spellcraft roll. Otherwise you assume that spells cast by your opponents are hostile to you.
The Protection from Evil spell has "Save: Will negates (harmless)".
The dominated person gets a save. No question here.
Will he intentionally fail it is the better question.
Dominate Person states "you can generally force the subject to perform as you desire". It also states "Subjects resist this control, and any subject forced to take actions against its nature receives a new saving throw with a +2 bonus." Clearly, the target wants to resist the dominate. If they know PfE is incoming, I think it is reasonable to allow them to automatically fail the save.
/cevah
A lot depends on how you imagine the "fluff" of dominate person. I'm picturing a subject that hasn't had his attitudes and allegiances altered, he just suffers from a compulsion to obey very specific sets of orders. Like a genie, he could look for loopholes in the wording of his commands.
This is how I run it.