Its practical. Shepard is running a multi-species squad through dangerous missions. He can't afford to have squadmates that might let their prejudices hurt the mission. For this reason, Ashley is a greater threat to the mission than Kaiden. Similarly, Wrex has to be eliminated if he can't focus on the mission parameters.
Not really. She's still pretty pro-human in ME3. She brings it up when talking about Cerebrus early on. She doesn't *hate* aliens, but prefers humans.