UPDATED: Seems like many folks have trouble of this sort in xcode 4, and the general solution seems to be to force the architecture you need and disable 'active only', which is what you had tried to do... but for the simulator, you need to specify i386 instead of arm*, like this:
xcodebuild ARCHS="i386" ONLY_ACTIVE_ARCH=NO -scheme temp -sdk iphonesimulator6.1
* ORIGINAL response which spawned comment thread below and still has some valuable reference: It sounds like your project my not be set up for 64-bit. You should be able to add arm64 to your valid architectures in your build settings and I believe xcode will automatically treat it as x86_64 for simulator builds.
For the second thing you attempted, you are hard-coding your architectures to IPhone architectures while targeting a simulator, which I believe is why the architectures are not available there.