Mostly I agree with the idea of providing some counter to the knockback effect of rocket launchers. Currently, the weapon doesn't do very much damage. Comparatively, it's pathetic, and only viable due to the range and knockback effect.
One potential solution (although not necessarily meant as a solution to rocket spam), as you suggested, is to improve stonewall to allow a specialized build to effectively counter the use of rocket launchers.
As a prediction, the advantage to the rocket launcher to the more effective bursting big guns is the reduced potential of friendly fire, which makes them far more viable in large groups, which does have the added advantage of juggling single or entire groups of players similar to the effect of Heavy Handed/melee knockdown builds, but would not necessarily be the main advantage. If we assess that adding a much higher chance of hitting targets between you and your actual target with the rocket launcher, which would add a chance of friendly fire near equivalent to that of other, bursting BGs, the rocket launcher loses its advantage of "rocket juggling" in PvP in large groups due to it losing its ability to be used en masse. Furthermore, the need of a specialized build --with one less perk choice due to one being dedicated to Stonewall-- defeats the purpose of making Stonewall prevent rocket launcher knockdowns. Although I definitely do agree that the perk should function like that merely because that's the purpose of its existence, something more conducive to the goal of the perk would be more productive.
Also, although not necessary, a perk which prevents the knockdown of a rocket blast should also prevent other knockdowns, just so it doesn't become counter-intuitive, as a measure of good game design (as opposed to whatever the 2238 devs were doing, not sure "bad design" does it justice.) This would provide a huge disadvantage to the already disadvantaged pancor jackhammer and would effectively eliminate the viability of heavy handed entirely. For this, changing Stonewall to something more specific to rocket launchers, or perhaps making it a support perk with high endurance + high SG or EW requirement (to avoid BG users simply taking it and changing nothing except for making heavy handed and pancors worthless), instead of the general "prevent knockdown" would promote better balance.
TL;DR: I agree that stonewall should serve its intended purpose provided that it should exist at all. I disagree that it should exist, as even changing it won't make it a viable counter to rocket launchers. In addition or instead, rockets should also have a much higher chance to hit targets between the user and the target, which prevents its use en masse to rocket juggle. Similarly, it would make it function much more similarly to other BGs, and its main advantage would become a reasonable counter to the popular low-hp sniper.
I would personally prefer Stonewall be made into a more specialized rocket-counter support perk for SG and EW, just so its use doesn't impede on already difficult-to-do viable SG or EW builds, at least compared to the brainless ease of viable BG builds.