What are some examples of companies that have abandoned Bitcoin payment processors in favor of in house Bitcoin integration? What are some examples of companies that have abandoned Bitcoin payment processors in favor of in house Bitcoin integration? 

For example which companies previously relied on Coinbase or Bitpay that now accept Bitcoin directly without the assistance of any 3rd party payment processors?
Some companies who have left cited privacy and security related concerns as their primary reason. It is therefore not surprising that some who have left the largest (and arguably most highly regulated) Bitcoin payment processors (Coinbase and BitPay) have chosen to remain anonymous:

https://www.reddit.com/r/Bitcoin/comments/3glqsx/after_using_bitpay_since_2013_to_run_my_online/

Here is a post from a Bitcoin Foundation member citing a need for improved privacy policies and more decentralization:

http://bitcoinfoundation.org/forum/index.php?/topic/1132-open-letter-to-bitcoin-businesses-why-im-closing-my-accounts/

Others may have moved to other providers that support more currencies than Bitcoin. This could be part of the reason Coinbase recently announced they will be adding support for Ethereum and Litecoin:

https://twitter.com/SatoshiLite/status/733531564852699136

My Google search revealed more merchants having accounts (involuntarily) closed by Coinbase, Bitpay, Circle, etc than merchants requesting a closure.  Since most businesses that accept Bitcoin online still convert it to fiat, the major payment providers offer a lot of convenience in terms of integration and currency conversion.