Right now we can beat a melee with proper timing/usage of CC & heals
No you can't. Not unless the melee is incompetent. When I am on my melee and I attack a Merc/Commando, they always die. Always. Well OK, that is a slight exaggeration. But excepting for the sort of cases where the melee is at half health and Merc/Commando is at full health, or the melee has all his abilities on CD, etc. the Merc/Commando should never beat the melee.
Now I am not a big fan of the "Run & Gun" suggestion since it helps the Merc Pyro not at all. But I was rather taken aback by your claim that the Merc could use that ability to heal 3 times in a row as a trump card. I mean seriously? Who cares if a Merc dps casts 3 heals? You don't think the damage output of a Carnage Mara or Rage Smash Monkey in 9 seconds is well over the healing from 3 Rapid Scans? A reasonable melee dps is more than capable of killing a Merc healer. He's going to make mincemeat out of a Merc dps who tries to be an ersatz healer.