“Michael’s pretty much discovered Megan and now he’s very quietly looking for her replacement. He hasn’t decided if he’s going to kill her off in the next movie, but he just wants to be prepared.”I recommend holding the moans (or celebration) as I doubt even so much as an outline of TF3 even exists. Right now I suspect Michael Bay, Ehren Kruger and others are still in the spitballing phrase and nothing is concrete except for a vague sense of what characters may return for the movie.
Megan Fox could choose to opt out of the next movie (being under contract for three movies doesn't really mean that much) so Bay would be wise to have a plan B under consideration just in case. However, Fox demonstrated she doesn't have the star power to open a movie with the box office failure of Jennifer's Body (to be fair the marketing of that movie was awful) so I don't see her turning down an opportunity to keep her fame flag flying high. Long story short, take this rumor with a grain of salt.
In a bit of a unrelated note, the above image is a before and after from GoodPlasticSurgery.com that shows a little plastic surgery can go a long way. Megan Fox had a tweak to her lips, nose and cheeks accounting for the change in look between the first and second films (beyond her tattoos). Makes you wonder if she has anything else planned before Transformers 3 gets before the cameras.