You might think that, if the will is evil when it is at variance with erring reason (because it is at variance with what the intellect perceives to be good), then the will must be good when it abides by erring reason. In fact, this is the first objection St. Thomas raises. That it's not the case, though, is because,
in order that the thing to which the will tends be called evil, it suffices, either that it be evil in itself, or that it be apprehended as evil.
"That it be apprehended as evil" is what happens when an evil will does not follow reason (whether right or erring). "That it be evil in itself" is what happens when the will wills something that is... er, evil in itself.
St. Thomas regards the question of this article as equivalent to
If then reason or conscience err with an error that is voluntary, either directly, or through negligence, so that one errs about what one ought to know; then such an error of reason or conscience does not excuse the will, that abides by that erring reason or conscience, from being evil.
But if the error arise from ignorance of some circumstance, and without any negligence, so that it cause the act to be involuntary, then that error of reason or conscience excuses the will, that abides by that erring reason, from being evil.
Hence, per St. Thomas, our wills can be evil even if we are following our consciences!