Turning mud back to dirt. It is perfectly possible in RL, yes, but far too damaging in terraria. The only way I know how to turn dirt into mud is to dig out every block and convert them in the crafting screen; this ends in a terribly deformed jungle. And the jungle must remain as some form of jungle so that the player can progress, as plantera, chlorophyte, and life fruit spawns nowhere else (and I know you can create an artificial biome, but it would still be terribly deformed and/or small unless someone spends days making a good one).
Three of the things the devs can do to fix this:
1- make three new biomes (corrupt jungle, hallowed jungle, and crimson jungle). (Like stated by the OP)
or
2- add a clentaminator solution that at least turns dirt and grass, and unpure stone into mud and jungle grass and pure stone.
or
3- make these biomes no longer interfere with jungle (like in the OP), until you could give something to help us out (like doing one of the above).
As for the players to alleviate the issue:
In pre-hardmode dig two wide trenches down deep, until you reach some point in the underworld, and fill them in with unnatural materials. They should be on either side of the jungle you want to protect.
Once hardmode begins, you may have to hastily produce more trench(es) if the biome's wall(s) have been compromised.
(Perhaps already suggested, but either way, this is the best I know of to shield the jungle. May take some work, but hopefully most of the original jungle would remain.)
Though at least the Jungle has enough core content, snow only some, desert.. barely anything.
