a mobile mjolnir is cannon fodder, no matter what is providing the engines. it would require so much cover to be effective that you'd be better off sending a warship.
Fine. Then let's mount that same beam in a cheap cruiser. And then let's hope hundreds of thousands of humans/vasudans will be "patriotic enough" to man them. On the other hand, it's not like the Fenris was able to defend itself, and yet the Alliance used it even in the frontlines.
Mass production of Meson Bombs would likely be the solution, but not as a form of conventional attack, they'd be put in mothballed destroyers in every system ready to seal off any node that Shivans were coming through as quickly as possible, or the system itself from the rest of GTVA space if it is overrun. Of course, this idea doesn't make for very fun campaigns.
The GTVA considered sealing off systems as just a temporary measure. I mean, you just can't run from the universal bully every single time he comes looking for a fight. You will end up with no systems whatsoever. Not to talk about what the economy will look like after 3 or 4 systems are cut off.
There's also a technical impossibility: Systems may have uncharted nodes.
If for some reason, they could not figure out the location of your fleet or your home planets, then you could eventually whittle them down if you found a tactic that they could not defeat.
Are you talking about guerrilla tactics in my Freespace?

If you abandon your planets and start hiding your fleet, you will end up looking just like the Shivans. Which kind of reminds me of my brother's theory about the Shivans being a future species "evolved" by genetic engineering from humans, that travelled back through time to prevent the destruction of their homeworld by this powerful and long-forgotten race of xenophobic aliens from their mythology. Well done, Shivans. Well done...

OFF-TOPIC ANSWERS
You need to get another look at your tables. The Perseus is essentially an Apollo MkII in regard of every single entry of the ships.tbl, aside maybe for the pitch and roll time, which are better by 0.1 sec for the old Ap', but this is compensated by, well, everything else.
The GTVA decommissioned the Ap just a little early, but we've got a more than excellent replacement for it right there.
Hmmm... I don't know. There's something in the Perseus that just doesn't cut it for me. I'm not sure if it's that I miss the Apollo's thin profile, or if it's just that I loathe the Perseus missile hardpoints and their "shuffle" when using Tempests.
I once "ported" FSport's Apollo to FS2Open so I could fly it in the Hammerheads' missions (and I loved it), though I admit I never tried to do the same in the Suicide Kings' missions.
Gimme railguns firing smaller meson projectiles 
GIMME LAZORS FIRIN' LAZORS!!!!!!!1Sorry, I just
had to do that.
