Avoid warnings about coupling when free_energy=no

At least during free energy testing it is irritating to
get a new warning about the molecule listed in couple-mol not
being decoupled when we disable free energy - that is why we
are disabling it. Changing the warning to a note, since it is
really a note to to help, not something that will result in a
bad simulation.

Change-Id: If56061be0ff784aeedfc31b92532927ab562392c