Fortunately, the appearance of metaphysical beings doesn't have to be logical. In the realm of possibilities, I would argue that just because we don't understand it, it isn't impossible. Therefore, anything is possible. Whether we like the answer or not.
A few possibilities
1) Just because it looks evil, it doesn't have to be
2) Maybe it is evil, and the good offspring were mistakes
3) Maybe it was changed to appear evil in order to rationalize the other gods decisions
4) Progenitor literally means parent or grandparent or anything above that in the family tree. Maybe it was renamed
5) Maybe it was imprisoned for other reasons than those mentioned, a coup (consider that everything we know about the progenitor may be a lie)
6) Maybe its physique was changed as part of the punishment
7) Maybe our three-dimensional perception simply isn't capable of percieving its true form
And so on