A MARV without weaponry ceases to be a MARV - at that point it's just a needlessly large and expensive harvester.
Yes, but that doesn't mean that no vehicle built
on the MARV chassis would be useless apart from a MARV itself. In this case, we're notionally discussing something built on the MARV chassis but bearing a mobile refinery. I don't know what we'd call it; I'm going to tentatively call it the MARV-R variant.
Such a vehicle is very much not "needlessly large," since we've been told no smaller platform can even carry the mobile refinery. Nor would it be "needlessly expensive," if there are sufficient benefits to being able to mount an APK mobile refinery and drive it into a Red Zone. It would merely be a different vehicle than the MARV, conveniently sharing a lot of parts commonality for ease of servicing and operations in a difficult environment.
Compare and contrast to the recovery vehicles various militaries operate that are built on tank chassis. Removing the guns (and often armor) from the recovery vehicle means it can no longer be used as a tank, but it is very much
not useless or "unnecessarily expensive," because it takes something with the horsepower and traction of a tank chassis to act as an effective tow vehicle
for a tank.
Some lighter sonic guns or other weapons might well be included on the MARV-R, to be sure! As you say, they are not useless. But doctrinally, the MARV-R would not be a frontline independent combatant operating without support, so it might well adopt lighter or different weapons.
My point here being, quite simply, that the MARV-R might represent a valid
variant on the MARV design, but would not be a valid
replacement for the existing S-MARV design. Not unless we could fit the refinery equipment in and still have room for nearly everything else the old S-MARVs have. Which would be delightful if true, but seems optimistic to me.
On the other hand, some modifications would almost certainly be integrated into the MARV-R, such as T-Glass and the U-Series alloys, just as a matter of necessity given that we'd likely be setting up a new production line anyway. With that in mind, work on the MARV-R might well be a stepping stone to a more ambitious and comprehensive "MARV Mk III" project that would fully update the Mk II "S-MARV" design and replace the old MARV-R with a new and still more capable mobile refinery variant.