I have a water treatment system (softener) that when it regenerates it drains into the septic system. I was told that the water going into the septic will kill the bacteria in the septic tank. If this is true why do they hook it up this way and what remedy is there for the drained water.

I have been in the water treatment business for 22 years and have heard this frequently. I also had the company that pumped my septic tanks ask about a water softener. I told them yes I have one. They blamed the septic problem on the softener discharge. After I told them my softener drains to a separate DRY WELL they had no explanation. There are many reasons for septic field failure. In my case the field had collapsed because it was 30+ years old and we use a LOT of water. There have been many studies on this subject, here are a couple links that reference this issue.
http://www.watertechonline.com/relatedinfo.aspx?id=7630
http://www.watertechonline.com/water-softening-conditioning/article/an-onsite-septic-system-is-your-concern-too
The only problem I have seen with discharge from softeners is with an engineered septic field.
A dry well for softener is relatively easy to install and works very well. You can find diagrams on line for dry wells if you choose to do your own.
RJ