That will happen any time that you have an enemy in sight who is capable of attacking you the next turn and the strongest defender in the stack is healing. Get someone stronger to guard him while healing, or move out of range of retalliation and he will heal without re-command (until a unit moves to place him in danger again).
I could check into making the system ignore enemy units who are in cities though, that one would be reasonable.
I just wanted to provide feedback on this change. It isn't a change I like. In the past I would find a forested hill and set my unit to heal and it would fortify until healed and It would become an active unit again letting me know it was fully healed. Until then It had the extra protection of being fortified from the heal command until it was up and running around again.
Now, when something walks up close it reactivates, IF it was actually fortifying it loses that bonus. Just as a enemy walks up and it needs it the most I have to run or fortify but I only get 1 turn instead of the 3 or 4 it had been sitting there.
To counter this I am now fortify the units I want to heal and hoping I remember to go back to them before they sit there for 40 turns forgotten.