Rather than remove the class, you can simply override the css. This is copied from bootstrap.css, but I have removed the transitions responsible for the slide down effect:
.modal.fade .modal-dialog {
-webkit-transform: translate(0, -25%);
-ms-transform: translate(0, -25%);
transform: translate(0, -25%);
}
Just include your css file after you include bootstrap's css. Here is a demo: http://plnkr.co/edit/MuIR7N51Zxe6dZFKomHq?p=preview