While it would be an overstatement to say that the Republican Party has been in a civil war since Boehner became Speaker, there's definitely been a great deal of friction between "establishment" Republicans--legislators like Boehner who were holdovers from the Gingrich-led "Contract with America" era (or earlier), and those who have joined Congress more recently. The younger members of Congress, many of whom rode the Tea Party movement and deep dissatisfaction with everything in Washington, the GOP included, into power, are generally more conservative than their predecessors, and less interested in making "compromises" with Democrats that still result in increased spending and an ever-growing federal government.
As a result, you had a situation in which the right wing of Boehner's party was often as big of a hindrance to his agenda as Speaker as Nancy Pelosi and the Democrats. Indeed, Boehner frequently worked closely with President Obama and Pelosi in an effort to get major deals done, only to find that he lacked the necessary votes of his own party. Although Boehner was well-liked on a personal level by most of Congress, he did not carry as much authority as one would expect from a Speaker, and struggled to keep members of his party happy.
I suspect that Boehner simply tired of this role, and also knew that present debate over government/Planned Parenthood funding had the potential to result in more intra-party fighting. This would almost certainly have provoked more conservative calls for Boehner's ouster at a time--little more than a year before major elections--when the GOP cause isn't going to be served by appearing irrational/unstable/leade