I'm trying to think this one through as well, I don't seem to have given the thought that it is due.
I see what you are saying. Measuring something at x and at y in one order or the other should not make any difference for spacelike separations. I would like to understand better the connection between applying the field operator on the vacuum and the process of measurement. What is the connection between the two?
But the key point is probably: what does one really mean by the expectation value of phi(x) phi(y) between vacuum states...In words, what does this quantity represent?
Measurements correspond to eigenvalues of Hermitian operators. Since we're dealing with a theory that is the quantum analogue of lagrangian field theory, any observable can be constructed from the fields because of Noether's theorem, which will relate our observables to symmetry currents. So if we want our measurements to be commutative over space-like intervals then our fields must be.
The operation \phi (x)|0\rangle doesn't have much to do with observation, it creates a particle state (I say "a" but there's really a sum of them as in Minkowski space-time we can expand the field as a sum over a plane wave basis).
If I write \langle 0|\phi_1\phi_2|0\rangle as, ignoring the exponentials and what not,
\langle 0|\int d^3k\left( a^{\dagger }_{\vec{k}}+a_{\vec{k}}\right)\int d^3p\left( a^{\dagger }_{\vec{p}}+a_{\vec{p}}\right)|0\rangle
then what we essentially have is the propogation of multiple "particles" between x and y, rather than just one of them, each described by a state a^{\dagger}_{\vec{p}}|0\rangle. Maybe it is the interpretation that is convoluted here, whether we interpret the momentum eigenstates a^{\dagger}_{\vec{p}}|0\rangle as particles or what may be interpreted as the position eigenstates
\phi (x)|0\rangle =\int \frac{d^3p}{(2\pi )^3}\frac{1}{2E_{\vec{p}}}e^{-i\vec{p}\cdot\vec{x}}|\vec{p}\rangle \simeq |\vec{x}\rangle
as particles.
I think that one possible reason for this apparent violation of causality actually being acceptable is that the field does not describe a or a system of physical particles. Only some or none of them are on mass-shell, so it is perfectly acceptable for these (intermediate, as in the propogator) "particles" to not follow classical physics and have the norm of their four-momentum as, say, a negative quantity. Afterall, QFT described systems of fields not particles.
The creation of an on-shell particle state by the field at x would be written \phi (x)|\vec{p}\rangle, which are usually drawn as external lines on Feynman diagrams.