At the moment the only way to fix the Dark node would be to grow a larger pure node via silverwood trees, some distance away and walk it to the dark node also via silverwood trees, then wait for the larger to absorb the smaller. Basically a huge amount of time and effort, it's not too bad to have a dangerous level of flux around it can cause the odd potion effect and lightning\mob spawn (wisps and really big angry zombies) so if you roof your living area and do not build in wood (also any farming golems better be under a solid roof the lightning specifically targets living entities and goes through glass) and can handle a bunch of wisps it's not a huge issue, the potion style effects are very short duration so they are not that much of an issue.