It's not a case of director/actor conflict for 'Ted 2', just a creative decision.
Seth Macfarlane is replacing Mila Kunis with Amanda Seyfried as the female lead in Ted 2. According to Deadline, Kunis will either appear in a small role in the sequel or not appear at all. Apparently there’s no bad blood between Kunis and Macfarlane. The casting change was just a creative decision and Kunis continues to provide the voice of Meg Griffin on MacFarlane’s longrunning Family Guy.
Kunis [l] is out, to be replaced with Amanda Seyfried [r].
There might be some dramatic twist coming in the Ted sequel, if Kunis’ character Lori Collins is no longer in the picture. At the end of Ted Lori married Mark Wahlberg's John Bennett, so there must be some shakeup in the story – either between the two movies or at the beginning of the second one. The rest of the primary cast – Mark Wahlberg and MacFarlane himself as the voice of the foul-mouthed teddy bear – are, of course, reprising their roles.
MacFarlane will once again voice the teddy bear.
The original film, released in 2012 went on to top box office records and make $550 million worldwide (this was in the pre-Iron Man 3 days). But MacFarlane isn’t risking the success of the sequel with an unfamiliar actress. Seyfried is already working with the writer/director/producer on his upcoming movie, A Million Ways to Die in the West, opposite Liam Neeson, Charlize Theron, and Neil Patrick Harris. Ted 2, which is still in the very early stages, is being billed for 26 June 2015.
Wahlberg, who had his career revived by the 2012 movie, is also reprising his role.