Personally I shall rue the day that Auto-charged jump-drives become the least bit serviceable. The whole point of jump-drives to me has been that one MUST drop-tools on clicking other things to make it charge. Effectively a ship has to disengage (at least where it's main weapons are concerned) so it can charge the drives, doubly so if an interdiction field is going strong and draining the system at the same time.
It means you can only charge one at a time, as well. Convenient as some things may be, they interfere with other elements of game-play, and I would not wish anyone to have to write exceptions for these conflicting interests.
Unfortunately for you, then, logic-drives are already serviceable. Hell, they're even balanced at this point in time. Now that the "overclocking" exploit is fixed, they can't charge faster than is manually possible, and they're very easy to inhibit with even the smallest of systems (2 blocks will out-drain most logic-drives). Logic-drives, in their current state, are simply a convenient system for shortening travel times, and they are well-publicized enough that everyone can benefit from this, if they wish to. Personally, I find this current state quite civilized. Fast-travel doesn't cause any harm, and, in fact, serves to make conflict or other player interaction more readily possible.
EDIT: I'm not all for the large drives, due to the size and space they take up, I can easily make something that can fit within the same space, and be able to travel a lot further, at the expense of a little charge time. Plus if the core pops off the drive still works. All you have to do is replace the core when you get to where you are going.
"Able to travel a lot further" is not true. Just about any well-built logic drive is able to travel continuously once initial charging is complete, assuming sufficient power generation. For yours to travel constantly, it would require a significant number of jump drives attached to the output; this number probably brings it close to, or greater than, the size of a compact and fast-clocked model such as Jaaskinal's own.
As to anti-lag, it's fairly easy to hook an unstable 0.5 second clock into a circuit which restarts the rail clock if it is not working. That will cause it to be on whenever the sector is loaded, and that's about all there is to do in terms of "anti-lag"; the rest will sort itself out whenever the server stops shitting itself.
Admittedly most rail-clocked logic-drives won't continue functioning if the core is shot off, but that's a fairly simple indicator that one is in combat, and a logic-drive won't get you out of combat anyway, if the enemy bothered to bring any sort of inhibitor at all.