I think what needs to be analyzed is how the weapon is broken in various modes.
In LMS/TLMS, you only have two shots of Atomic Fire's full charge shot. No pickups to regain ammo (unless I'm greatly mistaken and used to Classes LMS, which has no ammo pickups), thusly greatly limiting the weapon in comparison to DM: good aim is far more fundamental in this mode, if you miss a shot, might as well throw the weapon away. With the same drawbacks from DM in mind, anything but a OHKO shot is not rewarding enough for full charge, and this is further emphasized given the lack of ammo regeneration: perhaps only the 50 damage mid charge shot is more versatile for this mode, if you didn't have only 6 shots of it in comparison to Pharaoh Shot full charge shot's or Noise Crush full charge shot's crapload of them. Getting Atomic Fire in LMS/TLMS is, despite the OHKO combo possibilities, very unlucky as I've commented earlier on how less useful it is in comparison to the other charge weapons: I'd rather get these instead of Atomic Fire. If we only take into account LMS/TLMS, the changes you suggested would be a perfect fit, maybe add a slight ammo buff for it.
The possibilities of brokenness in other modes shouldn't be brought upon the table as reasons to nerf/buff this weapon, especially LMS/TLMS, where everybody gets it when you do, and not just you. Comboing an entire chuck of a team with a single Atomic Fire shot, or OHKOing "without prior notice" (this is bs, you can hear the charge sound very clearly, pay attention to your surroundings) in LMS/TLMS are, IMO, valid outcomes when you take into account how, in LMS/TLMS, you have no way to recover ammo or how easily spottable the player wielding the weapon becomes. Now in DM, you can recover its ammo, which makes the weapon more deadly.
Also, watzup's idea of being taken back a level of charge when hit is a very good idea, IMO. While in full charge, if you get hit at all, you're brought back to mid charge. 50 damage is still a decent firing output for a charge weapon, and not all the pressure of Atomic Fire is lost since, you know, 50 damage is a lot.