I have a lvl 50 bodyguard merc that I use for end game healing. I've healed all hard mode flashpoints, and regular and HM eternity vault.
Bounty hunter healing is excellent, and is definitely as good as operative and sorcerer. The main weakness of BH heals is the lack of any good AOE healing. Kolto missile is fairly unimpressive as an AOE heal, however it has the advantage of increasing healing received on targets with talents.
The main strength of mercenary healing is the ability to keep a tank alive. We get kolto shell, which heals the target when they take damage. With talents, our healing scan gives a 10% armor buff to the target. Our rapid scan is one of the most powerful heals in the game, and mine crits for close to 6k right now. Emergency scan is an instant cast free heal on a 21 second cd (18 with tier gear). This skill is awesome when you need some healing fast and your heat is high.
A lot of people who struggle with bounty hunter healing just haven't gotten used to the heat mechanic. It is extremely easy to overheat very quickly if you're not careful. However, once you get good at keeping your heat low, you can be an extremely effective PvE healer.
I've only done a bit of PvP healing, so I don't think I'd be able to offer any insight in that area. I hope this helps.