As you say, balance concerns! Or, rather - if that downside is toned down, there'd literally be never a reason to turn it off. As-is, it's already something you keep on much of the time, so based on that, I don't think it needs buffing, if you know what I mean.
I'd say it's on most of the time because traveling is slow, even inside systems it feels time consuming. I think that's of the route of that problem with it always being on. Going dark is great for sneaking, problem is it's 4 times slower travel. Maybe a solution would be to improve Go Dark/Emergency Burn and basic drive? Creating more reason to use them.
Is Sustained Drive too beneficial or are the other options too weak? Because slowing it down would make me install a mod asap. Raising the speed scale might help. 10/20/30 doubling the base ship speeds and having Sustained Drive/Emergency Burn be a +10 instead of a double(just a random thought), 10 would be a max speed fleet Go Dark, 20 a max speed fleet normal drive. If Go Dark had 10 speed possible with normal ships I wouldn't personally feel frustrated with my ships moving painfully slow feeling the need to Sustained Burn everywhere. If you did this you could lower the Turn radius from Sustained Burn and allow all skills to step forward in their intended roles. Sustained Burn would be for long distance travel and poorly suited for most movement in a system except crossing it. It also wouldn't make people pull their hair out on the forums because you'd be giving us something and not taking things away.
I'm aware this might impact system performance, moving faster means needing to load faster. I think people might like that if it's doable/balanced and/or doesn't conflict with existing plans.
edit:
On a current a 10 speed ship it would be 20 speed, doubled, in this example.
Go Dark = 10
Normal = 20
Sustained Burn = 30 (+10 instead of double, lower turn radius to suit it's intended role)
Emergency Burn = 30 (+10 instead of double, same turn radius as normal)