I'd lean toward discharging if you hold the shot too long. Having it break stealth as soon as you start charging would basically ruin them for PvE.
When talking about charge rifles I don't think they should break cloak. I'm guessing they would be similar to bolt action rifles but have an additional charge effect that would take even more time to get the max damage from. Adding all the delay hurdles together you pretty much have a one shot kill that takes longer to achieve than a cloak shotgunner IF you're skilled enough to land a head shot.
I'm just speculating since I have no idea how these new guns would function.
It would break the crit multi while stealthed perk. Seems it would make more sense in game mechanics for a weapon to only be able to hold the charge for a short period before discharging, like a BMG, and that discharge would break cloak. A sound effect for the weapon holding a charge would help balance it in pvp to give some alert of the danger nearby.
Balance is important, but that balance should happen without making charge weapons useless to someone using 1 of the 4 ego abilities, unless you want charge to also break the other 3.