Niles said:
The first term in H does not have a nonzero expectation value
Nor does the second term
I'm afraid I was too quick before and misled you. The Jaynes-Cummings model describes both the two-level atom and the radiation bath that it's in. The states ##|g\rangle## and ##|e\rangle## describe the atom, but we should also specify the state describing the radiation field, which is just a harmonic oscillator state ##|n\rangle##. The total state is a tensor product of these, which we could write in terms of ##|n,g\rangle## and ##|n,e\rangle##.
Now the density matrix has not been specified, so it can have off-diagonal terms ##\rho_{ng,me} |n,g\rangle \langle m,e|##. Expectation values like ##\langle a \rangle## (that would otherwise vanish in diagonal states) do not necessarily vanish in the presence of off-diagonal terms. So we should generally keep all possible terms.
Getting back to ##\langle \dot{a}\rangle ##, the first term in
$$\text{Tr}(-aiH\rho + ai\rho H) = i \left\langle (Ha - aH) \right\rangle $$
is
$$ i \Delta_c \left\langle (a^\dagger a a - a a^\dagger a) \right\rangle = - i \Delta_c \langle a \rangle,$$
where we used the commutation relation ##[a,a^\dagger]=1##. This term is the one proportional to ##\Theta## in (5).
The second term, proportional to ##\Delta_a## vanishes because ##[a,\sigma_\pm]=0##.
The third term might as it contains aa^\dagger = 1+a^\dagger a. So now this term says
<br />
g_0 ((1+a^\dagger a)\sigma_- - aa\sigma_+)<br />
I'm not sure how to evaluate the trace of these two terms. I would really appreciate a hint.
It helps to write all similar terms down at once using the commutator. There's a term involving ##\langle [a^\dagger,a] \sigma_-\rangle## and a term with ##\langle [a,a] \sigma_+\rangle##. We don't need any details of the state to reduce these to expressions involving just ##\langle\sigma_\pm\rangle## .