I would like to point two things out.
The first is that Bay is producing the movie. He's not writing it, and he's not directing it, so I find it highly doubtful that the origin story revision was his brainchild. The second is that Bay has stated that one of the original TMNT creators (he didn't refer to the person by name in the material I read, but I suspect he's talking about Laird) is working closely with the writing team to help revise the Turtle's origin story. The explaination might be as simple as 'they were four alien brothers who touched the mutagen and then touched a turtle', which is pretty much exactly the same as Splinter's origin in the '87 series, minus the alien bit. Frankly, there's a lot of ways that this revision can still do justice to the source material.
There are no bad ideas, only poorly executed ones, and knowing nothing else about this project I don't think we have enough context to make a call on whether this idea is being mishandled or not.