Negative energy density in QFT
The energy density is not necessarily positive definite in quantum field theory (refs 1 and 2), not even in a representation where the total energy is positive definite. Reference 1 says this on page 2:
quantum fields have long been known to violate all such pointwise energy conditions... and, in many models, the energy density is in fact unbounded from below on the class of physically reasonable states.
This occurs even in the simplest model of all, the free scalar field. In this case, the result might seem surprising at first, because the naive expression for the Hamiltonian (total energy operator) is the spatial integral over a manifestly positive-definite integrand. The catch is that in order to make the total energy finite, we need to subtract a constant term that depends on the high-energy cutoff used to define the theory. (We can do this without any mathematical ambiguity by treating space as a very fine discrete lattice, for example.) This constant diverges as a function of the cutoff, so even though the naive energy density is manifestly positive definite, the energy density with the required constant term is not.
What about gravity?
What are the implications for gravity? I don't know. That's a tricky issue for more than one reason. But since the question asks specifically about the Standard Model instead of about a nonperturbative quantum theory of gravity, I'll mention this: The usual ways to account for gravity in the Standard Model are
Treat the metric field as a prescribed background field, in which case it doesn't care about the energy density (or total energy) because it's prescribed.
Treat the metric field as a quantum field, but only perturbatively (small-coupling expnansion), in which case it still doesn't even care if the total energy has a lower bound. Perturbation theory works fine for models like the $\phi^3$ model, whose total energy cannot have a lower bound.
Nonperturbatively, one of the basic principles of quantum field theory in flat spacetime is that the total energy must have a finite lower bound, so models like the $\phi^3$ model are not allowed. The appropriate way to generalize this total-energy condition to a curved spacetime background is a topic of current research ("total energy" is ambiguous in a generic curved spacetime), and identifying a good set of general principles for nonperturbative quantum gravity is also a topic of current research.
Non-negative total energy in QED/QCD
By the way, to prove that the total energy in QED/QCD is nonnegative, one approach is to use the path-integral formulation. After Wick rotation to Euclidean signature, we can show that the action has a property called reflection positivity, and then we can appeal to a general theorem about the existence of a representation on a Hilbert space with a Hamiltonian having a nonnegative spectrum. This is explained in ref 3.
Fewster (2005) "Energy Inequalities in Quantum Field Theory" (https://arxiv.org/abs/math-ph/0501073)
Fewster (2005) "Quantum Energy Inequalities and Stability Conditions in Quantum Field Theory" (http://arxiv.org/abs/math-ph/0502002)
Montvay and Münster (1994), Quantum Fields on a Lattice, Cambridge University Press