As far as I know, there was a Hera Torpedo at some point, though it was removed again. This torpedo was supposed to be the only device capable of disrupting JDs, though I would personally feel like that would make it too hard to disrupt a jump charge. I personally see no issue with the charge being able to be disrupted with any CD.
The alternative would be always needing a ship with that one piece of equipment with you when a JD is used offensively against you, or you lose half your ships. That is realistically never going to happen, just as people prefer cloaks over cloak disruptors. The former gives you acting potential, the latter only reaction potential and therefore limits you. People will never chose a Hera over a CD or torpedo (if they are implemented again). Having CDs work like that is a good compromise.
Well, if they are used offensively. I just have flashbacks of certain people trolling a group jump like it happened every so often in the Uncharted events.
According to Spazzy, they are supposed to be used offensively. The best way to counter mindless trolling is to make it easy, not harder, to disrupt the charge for a jump, which you can do by allowing CDs to disrupt them, as is currently the case. It would also make the payoff for a successful combat application of the device feel way more rewarding if it was a challenge to pull off and encourages team play and coordination.
The problem with that is that the cloak disruptor is still just a reaction piece. While a cloak or a JD gives you opportunities to act, the cloak disruptor is only useful in reaction to something someone else does. Inversely, that means that it is useless unless you are facing a situation in which you can expect these things to be used against you, and for such cases, you would really rather have a cloak yourself or a CM.
Spazzy once made a remark about making cloak disruptors a piece of equipment like the JD that is mounted on an equipment slot, or just fixed to the ship like an armor upgrade so it doesn't take away the CM slot. That could solve this issue, but until that is feasible, I remain against the idea that CDs shouldn't be able to disrupt the charge time.
It should be noted that the mechanics of disrupting a charge hasn't changed.
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Why not add a CD to the Cloak Disruptor, similar to the Cruiser Disruptor Platform, then? That would turn it into a mighty AoE support weapon, being able to interrupt cruise, cloak and jump.