The two years ago my cover got really beat up, and the cover wasn't a barrier. So, when I pumped the water off the cover, I ended up dumping a good bit of pool water as well.
Last year I ended up letting more water from the cover into the pool than I wanted to, but the only consequence was that it took and extra day or two to clear. No algae, but I also started chemical additions very early, so the water was very cold.
This year, my cover is now completely shredded around the edges from the snow and wind, so there's no way to prevent mixing. While there are a lot of leaves in it, the water on top of the cover is clear. My plan is to hook up plumbing and start balancing the water in the next few days. After a couple more weeks when the nights start to stay a little warmer, I'll skim the leaves off the top, but let the water from the cover stay in the pool.
My theory is that even if there's a small amount of algae living in the "cover water," it will only amount to about 5% of the volume of the correctly balanced bulk pool water, and won't have much more of an effect on the chemistry than a cpmparable amount of rain.
That's the long story. Short answer, if you drain it, drain it to the yard. Don't put it in the septic system.