Has the legitimacy penalty actually stopped any of you from marrying the first lowborn genius you find?

For me it does not even factor in, especially if I start as a small realm (which is almost always). The long term benefits of having genius for the rest of the game is just too much for me to give up, combined with a good stewardship wife, and guaranteed 4 star educations for the whole game (genius on the guardian and ward basically guarantee it if they have the right childhood trait), which you can instantly upgrade to level 5 at university when succession kicks in.