It's been my experience that chlorophyte does a pretty mediocre job of halting the corruption. It can, at best, create a stalemate with a corrupted area. I've never seen chlorophyte actually reclaim a corrupted area, probably because chlorophyte has maximum density limits and corruption doesn't.
Incoming wall of text:
My actual solution is to create corruption barriers around the worldgen biomes before entering hardmode. This is usually done by making a 5-width tunnels all the way around its edges. (You technically only need a 3-wide gap, but making it 5-wide prevents it from jumping across corners and gives you a bit of a buffer if you mess up.) I find that to be much easier than doing any shenanigans with the Clentaminator, plus you get to keep your biome for materials. You might need to be careful about corrupted grass, though, since the vines that dangle from the ceiling and the thorny vines that grow from the floor can both spread the corruption. If you've got a Drill Containment Unit, this process takes less than five minutes. If you don't, it takes a bit of time.
The REAL danger to the jungle comes from the diagonal columns of hallow and corruption that spawn when the WoF is defeated. Since these have some variation in where they spawn, I normally just back up my worldsave before killing the WoF, save and exit after he's dead and I get the announcement of light and dark, and check it in a world viewer. If the corrupted column goes right through my jungle, I'll reload and kill the WoF again. Note that the hallow going through the jungle is perfectly fine because hallow can't affect mud at all, but it means you probably won't have much surface hallow which will make getting unicorn horns and pixie dust harder.
Once the columns are in acceptable positions, I dig four more barriers, one on each side of both columns, again 5-width at the edges. If you do this immediately after the WoF is defeated, the lines will be very well-defined and you can preserve your cavern layer with (relatively) minimal effort. Note that this is significantly more time-consuming and dangerous than the pre-hardmode barriers, even with a Drill Containment Unit, because you'll be undergeared at that point. The longer you spend gearing up before doing this, however, the harder it will get, because the irregularities of the underground will cause the corruption to spread out unevenly, so you won't have the nice clean diagonals. On the bright side, you should have a good supply of souls and cursed flames or ichor once you're done, and that can really help later on.
In conclusion, it's a lot of work, but it is absolutely worth it. You get to preserve and separate all of the biomes, and retain control over your world. Since Terraria is all about manipulating the world to your benefit, it seems to me like a very worthwhile task.
You can't really account for or predict the corruption/hallow that spawns when you break a shadow altar, unfortunately. You just have to be vigilant, or use a world viewer to find them after they've spread out enough to be noticeable on the map, then dig down and clentaminate them.
Post edited July 03, 2016 by bevinator