It would be more like 1/4 similar mark fortress hitpoints at most, with far fewer shots, damage per shot, and range.
I was intentionally going for that kind of power to reduce the number of times players will actually have to rebuild, but to allow for enough incentive in building things for there to be a significant associated penalty in losing a command station.
I'm not sure how much it would slow down the early game if we're talking 5 minute build time for mk1. That would be 20k metal/crystal per minute, ~333 per second which, okay, may be a bit much drain per second, but the numbers can be fiddled with to make them more okay. From what I've seen in player reports though, most players are not taking any planets in the first 10 minutes of the game (destroying, maybe, but taking?), and if they play like X they're taking 1 planet every 40 mins or so. That's completely doable, I think.
An alternative, though one that wouldn't really fix the main issue being discussed here (how to reduce the number of times one has to build command stations) would be to leave mk1 as is (cheap, throwaway command station) and have an exponential type increase in power. Not a solution that I think would be desirable though.
Increasing cost to build for every additional command station would end up being ridiculous if command stations are still being lost at the same rate, because it'll run players out of resources extremely quickly. Again, I think the point of this discussion is "how to make it so we don't have to rebuild command stations manually so often." Automation is one way (which I don't think will happen), and making it so command stations don't have to be replaced as often is another. The numbers can, of course, be fiddled with if I've taken the idea too far in both directions. Straight up penalizing players for rebuilding command stations too often will end up driving players away though.
Edit: Thoughts on command station weapons
Military: Leave as translocate, but boost number of shots(probably not) or damage(would need to be a very large boost to make it noticeable, though a mk3 military wouldn't necessarily need to be under a forcefield if it had the 15 million hitpoints suggested by 1/4 fortress mk3 health)
Logistics: 1x/2x/3x spider-style shots (depending on mk level). Sticks with the theme of slowing enemy ships down/causing mobility problems, and won't be so ridiculous that it's disabling entire fleets super quickly.
Economy: Large number of short range (7000 or less), low damage armor rotting shots. Makes it clear that economy station is not there to deal damage, but it can provide a minor bonus to friendly ships operating on the same planet.
All of these shot types follow under the idea that they should be useful even while a command station is under a forcefield, which means that pure damage will never be useful. The economy station defensive guns in particular are a last ditch defensive measure, since they can't really do anything by themselves. In addition, with only one command station per planet, there shouldn't be too much of a problem with any of these weaponry changes making them overpowered.
Edit2: Command station health could run as something like:
Military = 1/4 same mark fortress. Mk1 = 5 million, mk2 = 10 million (?), mk3 = 15 million (assuming I'm correct in remembering fortresses have 20/40/60 million hp each).
Logistics: 1/2 military station health.
Economy: 1/5 military station health.
Econ will still be relatively easy to kill, but military will require a concerted bomber assault.