There's nothing in either the Magic Circle spell description or the Unhallow spell description to suggest that outsiders cannot be called into the affected area. In fact, as I re-read the Magic Circle Against Evil spell, it's not clear that the spell even hedges out outsiders summoned/called outside it ... It just says that everyone in the area gets the benefit of a Protection from Evil spell, which means they can't be touched by the outsiders. So, in the standard configuration, the alignment of the outsider certainly does matter, because it does in the Protection from Evil spell. (Note that, under this reading, if the evil outsider is in range when the spell is cast, it also gets the benefit of a Protection from Evil spell. Which means it can't be touched by non-good outsiders. Which means it can't touch itself. [What's so funny? Perv!] There's got to be some kind of tactical use for that.)
In the 'confining circle' configuration, the spell does create an impassible (for the outsider) barrier. (By the way, this use specifically applies to called creatures in the text of the spell, so it definitely does apply to outsiders called by the Gate spell. Why anyone would do this is another story-anyone who can cast Gate can use the spell to control called outsiders of less than 35 hit dice anyway, and I don't think a third-level Magic Circle spell will last long against a 35+ hit die outsider ...) The text of the spell does not limit this use by alignment, so technically you could trap a Neutral Good outsider with a Magic Circle Against Evil spell, which could not otherwise affect it in any way. If you think this is how it is intended to work, well, fine, whatever. By the text of the spells, a true Neutral outsider can only be hedged out by a Protection from/Magic Circle Against Evil spell, while Lawful Neutral and Chaotic Neutral outsiders have the distinction of having the only alignments that are subject to two protection spell types.