Simple: preemptively reinforce your systems in anticipation of being undermined. You know it's going to happen, so plan accordingly. You can even counter data download sniper undermining using the same mechanic as the underminers; download data yourself, sit on it until 1 hour before the tick, then redeem it to suddenly boost the reinforcement of a system. That you choose NOT to download data at surface settlements as one method of counter-undermining is just that; your choice. A choice the rest of us are not constrained by.
If your counter-argument to the above is, "We can't possibly reinforce ALL our systems!", here's my counter-counter-argument (and the fundamental crux of the problem):
If the number of systems under your Galactic Power's control is greater than what the Commanders pledged to that Power can reasonably reinforce / defend, then perhaps their territory is larger than it should be. If your reach exceeds your grasp, it should be expected you're going to lose some of it until you achieve equilibrium; a case of perhaps a little culling being called for.
Once again, your inability (or, rather, your Galactic Power's collective pledgees' inability) to adequately defend its current territory is a you problem (collectively, your Galactic Power's problem). Your solution is to expect everyone to conform to a set of rules that favors your preferred play style and gives you an advantage. To wit, playing Euro Truck Simulator in Space, peacefully shuttling mined commodities and/or PP Allocated Resources back and forth ad nauseam, with the expectation of achieving uncontested reinforcement and unfettered expansion; all while placing artificial constraints on data download undermining so as not to interrupt the reinforcement effort nor inconvenience you. This isn't Power Play 1.0 anymore.
You claim data download sniper undermining isn't "fair". News flash: this is a 12-way WAR; whether cold or otherwise. There's nothing fair in war. Is it fair that some Galactic Powers are smaller than others and can't out-compete the efforts of larger ones? No. But that's also part of war; some nations are larger than others, have greater population, have more natural resources, greater industrial capacity, etc., etc., etc. So you avail yourself of any and all tools at your disposal to give yourself an edge wherever possible. For smaller GPs one such tool in the toolbox is data download sniper undermining.
Now, all that said, I'd be OK with a mechanic added that, when a Commander attempts to download data at a settlement in a system controlled by a Galactic Power, an alert will go out to players pledged to the targeted Galactic Power IF the Commander attempting the download neglects to disable the settlement alarm or one of the NPCs calls in an alarm before they can be silenced.
I'm all for play and counter-play; the more direct and immediate, the better. By which I mean I had stated earlier that undermining can be countered by reinforcing; which - though I still stand by that as an available counter - is indirect, not very dynamic, and six-degrees-of-separation. Something more direct, immediate, and in real-time in the form of the aforementioned Galactic Power-wide alert I'd be OK with.
Even if the underminer(s) are in Private Group or Solo, the alert would still be sent. Though the underminer(s) themselves might not be stopped, it at least puts the pledgees of the GP being undermined on notice that, "Hey! Someone has raised the alarm in a settlement in system XYZ!" Then we add another layer of counter-counter-play: intentional feints at undermining to draw the targeted GP's members' attention to system XYZ and away from system ABC, for example.
Or maybe it's an Odyssey mats farmer who is just there to collect data for a suit or weapon upgrade. You, as a pledgee of that Galactic Power, won't know the difference. Do you investigate? Do you treat it as a false alarm and ignore it? This further reinforces the notion that Power Play Commanders should be active participants in patrolling, securing, and maintainting their Galactic Power's territory rather than expecting it to run on auto-pilot without their active involvement.
TL;DR: Qouted Commander believes sniper undermining of Power Play systems through settlement data downloads isn't "fair" and wants limitations placed on it. This is a 12-way WAR! Of course it's not fair. Besides, a counter to it already exists in the form of system reinforcement and/or performing data downloads of their own.