You are correct that there is more gravitational work done on A than on B in the setup that you made. The other answer is correct that the gyro is not going to spin faster just as a skateboard wheel will not either when you drop the skateboard.
The problem in your analysis is that what causes a gyro (or any wheel as mmesser314 says) to spin faster (or slower) is the torque about the axis of rotation. In this case, there is no torque about the axis because the two masses are the same and the moment arm is the same (and obviously the gravitational field is assumed uniform everywhere). The rate of rotation is not a function of the difference in work on each mass.
If you feel unsatisfied because this seems like a bit of a puzzle, that is because it is. The difference in work on each mass leads to a feeling (an incorrect one) that one mass should move faster than the other. This does not happen because when you consider the masses individually, you must consider the force of the rod connecting the two. When the entire gyro is considered, the tension in the rod is an internal force and so can be ignored, as it cancels out acting oppositely on each mass. However, the motion of each mass individually requires this internal tensile force, which is equal and opposite between the two.
This is especially tricky, because people are used to the idea that centripetal force does not to any work, but it does do work when viewed from a reference frame where the center of rotation is moving, such as this one.
I promise that if you consider the work of the tension provided by that rod on each mass in addition to the work done by gravity on each mass, you will find that the system can "keep its shape" (meaning the center is colinear with the two masses) and continue rotating at the same rotational velocity. The extra energy due to the whole system moving down through the gravitational field will be accounted for with acceleration of the center of rotation, just like when you drop the skateboard in the example from mmesser314.
If you don't believe me, I can work this out for you, but if that seems a bit too much and you are happy with this explanation, I will leave it there.
EDIT: Since you asked, here is an energy conservation check. We will assume, as stated, that the rotation is independent of the free fall in gravity. The gyro will start at the origin as shown in your first picture, with X right and Y up. Thus, the center of the gyro moves as a point particle with:
$$
\vec{r}_{G} = -\frac{1}{2}gt^{2}\hat{e}_{y}
$$
and the individual masses are given by:
$$
\vec{r}_{A} = \vec{r}_{G}-L\hat{e}_{r}
$$
$$
\vec{r}_{A} = -L\cos(\theta)\hat{e}_{x} -\left(L\sin(\theta) + \frac{1}{2}gt^{2}\right)\hat{e}_{y}
$$
and we note that since the rotation rate is assumed constant, we can substitute $\theta = \omega t$ at any time. I will do the calculation for mass $A$, but you can repeat it for $B$ if you want using:
$$
\vec{r}_{B} = \vec{r}_{G}+L\vec{e}_{r}
$$
$$
\vec{r}_{B} = +L\cos(\theta)\hat{e}_{x} +\left(L\sin(\theta) - \frac{1}{2}gt^{2}\right)\hat{e}_{y}
$$
The total force on $A$ (both gravity and the rod, where the rod must be standard centripetal), is
$$
\vec{F}_{A} = mL\omega^{2}\hat{e}_{x} + m\left(L\omega^{2}-g\right)\hat{e}_{y}
$$
Differentiating the position of $A$ from above, we find its velocity:
$$
\vec{v}_{A} = L\omega\sin(\theta)\hat{e}_{x}-\left(L\omega\cos(\theta)+gt\right)\hat{e}_{y}
$$
With this expression for $\vec{v}$, we find
$$
v^{2} = L^{2}\omega^{2}+g^{2}t^{2}+2gL\omega t\cos(\theta)
$$
Remembering that $\theta = \omega t$ we can get the kinetic energy as a function of time:
$$
KE = \frac{1}{2}mL^{2}\omega^{2}+\frac{1}{2}ml^{2}g^{2}t^{2}+mgL\omega t\cos(\omega t)
$$
You should note that the first term is just the gravitational free fall of the whole gyro as a particle, the second is the rotation, and the third term is purely oscillatory. So the kinetic energy oscillates around the sum of the energies of the two motions.
The change in KE between any two times is then:
$$
\Delta KE = \frac{1}{2}mg^{2}(t_{2}^{2}-t_{1}^{2}) + mgL\omega\left(t_{2}\cos(\omega t_{2})-t_{1}\cos(\omega t_{1})\right)
$$
Now, the trick is calculating the work, which is what you were asking. This is by definition:
$$
dW = \int_{\vec{r}_{1}}^{\vec{r}_{2}}\vec{F}\cdot d\vec{r}_{A}
$$
$$
dW = \int_{t_{1}}^{t_{2}}\vec{F}\cdot\vec{v}_{A}dt
$$
$$
dW = \int_{t_{1}}^{t_{2}}\left(mL\omega^{2}\hat{e}_{x} + m\left(L\omega^{2}-g\right)\hat{e}_{y}\right)\cdot\left(L\omega\sin(\theta)\hat{e}_{x}-\left(L\omega\cos(\theta)+g\right)\hat{e}_{y}\right)dt
$$
which will clean up to
$$
dW = mg\int_{t_{1}}^{t_{2}}\left(gt+L\omega\cos(\theta)-L\omega^{2}t\sin(\theta)\right)dt
$$
Upon evaluating the integral we get
$$
W_{12} = \left.\left(\frac{1}{2}mg^{2}t^{2}+Lg\sin(\omega t)-Lg\omega^{2}\left(-\frac{t}{\omega}\cos(\omega t)+\frac{1}{\omega^{2}}\sin(\omega t)\right)\right)\right|_{t_{1}}^{t_{2}}
$$
which cleans up to
$$
W_{12} = \frac{1}{2}mg^{2}\left(t_{2}^{2}-t_{1}^{2}\right)+mgL\omega\left(t_{2}\cos(\omega t_{2})-t_{1}\cos(\omega t_{1})\right)
$$
It is evident that work done on mass $A$ between any arbitrary times $t_{1}$ and $t_{2}$ is equal to the change in kinetic energy between those two times. This means that the assumed motion is consistent with the work energy theorem. The assumed motion was, of course, simple constant rotational motion and simple point particle free fall in gravity, decoupled from one another.