えー？ does mean "whaaa?" However, ええ, used here, means "okay." The middle line is not a lengthen, it's just one of the three sound lines.
They all look incredibly guilty. They know what they did. They know that Miko knows what they did. They've been caught and are not even arguing.
I'll leave it as is, but do know that I gave this some thought before I changed it. I would argue your last point as their final expressions are not explicitly shown. However, my main reason for changing it was that I have only seen or heard ええ used to mean "okay" in the "yes, that is correct/yes, that is so/sure/confirmation" context, whereas in this situation the only "okay" that would really make sense is of the "yes, I understand/I accept" variety. And that would much more be in the realm of an elongated はい than an ええ. So I think if the artist wanted to impart a meaning of "okaaaay~," he/she would have opted for はいー.
In addition, you may notice that the second え is smaller than the first, which I usually interpret as a sound extension rather than an additional character which completes a word.
Here are two posts of Nichijou's Annaka where her trademark "eeeehh!?" has been portrayed using えぇー : post #1123811 post #959501
