Here's a
thread I had on a similar topic - although that was whether she
was actually mad, rather than preventing her lapse in the first place. Interestingly enough, her mother deserves just as much blame (apparently) as what's been heaped on her husband and father through the centuries.
As to her being Protestant, it wasn't so much Protestantism that she was in favour of or against Catholicism, merely she prefered the French brand they had in Burgundy to the dry Castilian version. Once she was incarcerated, after the Communeros, there was a gallery of the palace devoted as a chapel. Juana first wanted it decorated a la Burgundy, then threw a hissy when it was, and they stripped it down to a la Espagnol, and she threw another hissy, and finally they just sorta left it. What she would do is go to chapel, but refuse to take the host,
however she would insist that inspite of it bypassing her, it be offered to the Infanta Catalina.