According to what I've read, Apple is saying that they have bought the rights to use the patent and that they will defend their right and everyone else' right to use the patent.
Here is Apple's CEO's letter to Lodsys as posted in MacWorld:
http://www.macworld.com/article/160031/2011/05/apple_legal_lodsys_letter_text.html
Here is an article, in MacWorld about the issue:
http://www.macworld.com/article/160030/2011/05/apple_lodsys_license.html
Some of the major developers have expressed "relief" that Apple is at the forefront of the fray.
<EDIT>It is noted in one of the articles that, Rovio, EA, and Atari are involved in protecting the use of the patents also.</EDIT>
In-App Purchase is currently being used by many Apple partners. Apple can't let this go against them so there will be a satisfactory settlement, one way or the other.
All that I would ask is to know that it will be included with AppGameKit unless there is a judgement against Apple.