I can't answer from direct play, but using the skill calculators and the baseline skills for both classes, they all do the same amount of healing, just in different ways.
The Jedi healers have high output spells designed to heal one person a lot at a time, with a few group heals at the higher levels.
The Fringe healers (operative/scoundrel) heal over time, so you are healing multiple times over the course of a few seconds, breaking your casts up, and they seem more stackable.
The Tech healers (mercenary/commando) seemed to be based around group healing with a greater chance of scoring critical heals.
All three groups pump out around the same number of hit points over time, so I think the one you chose should be based on how you want to deal with the aggro. From direct play experience, I know that our jedi healer pulls way more aggro at a time than our operative healer. She heals with fewer abiility presses in each fight but they are spread out though the fight, while our operative tends to front load the healing and then spend the rest of the fight sneaking around and dropping people from stealth. I haven't played with the mercenary yet, so I can't speak to the actual in game tactics.
Having now played through fifty and with a few more alts running around, I have learned that the above holds true but the force users with a tweaked build are in fact capable of pumping out more healing than the others, although the edge is only about a percent. Also, If you are going healer, biochem makes you better by about ten percent and allowing you to self heal with reusable medpacks that don't draw aggro. At least until it gets nerfed again.