As some communities, e.g. the Ruby community, is approx. based 99% on github, I fully understand and have a strange feeling myself. Time will tell if TPW and AH can work together and make an even bigger success.
But how can we know that's even an issue? There are a hundred hypotheticals here (both positive and negative), and focusing on the ones that would only be the case were Andreessen Horowitz & GitHub unwise companies seems unnecessarily negative.
Now, if there were reason to think any of them, that'd be one thing. But we only know there was a huge investment in an awesome company from a great VC firm.