The KS system name backers will no doubt have their moniker applied within the Core systems - there's a major difference between having a frontier mining system with a corrugated iron & duct tape outpost named after you, and a Core high-tech and tourism world with 50 million inhabitants!
The honour of having an already bustling and inhabited system at game launch bearing their name is really what that KS pledge tier was about, I feel.
When it comes to naming beyond the frontier, I see a relatively simple compromise : as things stand, unexplored systems have catalogue names, appropriate for their location within the galaxy. Players of Elite Frontier will recall all systems, no matter where they were in the galaxy, had names thanks to the random generator.
Seems logical to me to implement a system in ED where currently catalogue designated systems already have names, just 'under the surface' as it were, waiting for a player to scratch the catalogue number off.
Okay, so that means players don't get to actively name a system, but their Commander name could still be listed on the system's info page in a "discovered by Commander XYZ" note.
Using this system, it would make it immediately clear on the galaxy map which systems had been visited, because they'd all have a name rather than a catalogue number. It also saves dev resources because the system would essentially be automated, requiring only a Commander's name and the system's own 'hidden' name - both of which the game already knows.
Okay, okay, I can hear the grumbles, and fair enough, the protocol I've outlined above does seem a bit of an unsatisfying cop out.
But here's another compromise - the point of discovering systems is that eventually the AI will send out mining ships and station builders to those systems. And when that starts happening, I think it's only logical that a planet or moon within a system could be named after the Commander who first visited the system.
Anyone who's explored the edge of colonised space in Elite Frontier will remember names like "Nakasone's Rock", "Bradley's Wreck", and "Harrisonworld" that all were obviously generated by the same maths as any part of the game that required NPC names, like the mission bulletin board for instance.
So here's the really beautiful part - if ED's code can be set to acknowledge the discoverer of a system, it means it already has the Commander's name attached to that system (because it'd be on the 'Discovered by' section of the system info of course). From there it takes minimal effort to automatically rename the primary interest planet or moon of a discovered system as soon as the AI gets there and sets up a permanent facility.