I would say 'yes'. But I'll start with the 'no' side:
The Conjuration school description lists 'Calling' and 'Summoning' as separate schools. But the spell description for the various Protection from [Alignment] and Magic Circle Against [Alignment] spells only talk about 'summoned or conjured' creatures. Gate is a Conjuration (Calling) spell-since the other spells don't refer to 'called' creatures, gated outsiders should be unaffected.
Now, on the 'yes' side:
The spells say 'summoned or conjured'. This would naturally be read as referring to the whole school. So any called, created, or summoned creature would be affected by the spells. (Why they specify 'summoned' specifically when 'conjured' would include 'summoned' as a subschool is inexplicable.) The clincher to me is that the Calling section in the PH (pg. 157) lists the various Planar Binding spells as examples where the magic circle spells are useful. And those spells are, in fact, listed as Conjuration (Calling) spells in their descriptions. (Before anyone with an old PH jumps me-Planar Binding was erroneously listed as Conjuration (Summoning) in the first printing, but it has been changed to Calling in the errata and in the second printing of the PH.) So clearly, the magic circle spells (and by extension, the protection from spells, which are supposed to work the same way) work on called as well as on summoned creatures.
Summary: per the PH pg. 157, the magic circle spells work on creatures called by the planar binding spells, and by extension should work on gated creatures (all of these spells are of the same type).