So it turns out, if you rush the nether simulation, and break the magma cube spawner before it can spawn a 'cube, there is no other way to kill a magma cube to progress, and you are softlocked. (Unless you spawn one in with cheats)

Message I got every time I broke a spawner: (last spawner spawned a blaze boss which I killed)

Message I got when I tried to enter the nether portal:

Living Magma quest:

I hated those godawful mosquitoes though.