I have a couple PoD to propose for protestant France, which are more original that the Henry IV ones :
+ The Guise take up the flags of protestantism instead of radical catholicism. At one point they were thinking about it and it would have enabled them to size considerable church properties. OTL, the Guise chose to come to power by being more catholic than the king; What if they choose the other way. Of course, by reaction, it will cause for OTL protestant lords to become catholicism's champions. But the Guise main lands and center of powers were to the east of france, so they can link much more easily to the german and dutch protestants.
+ Francois II's court converts to protestantism. The Guise at one point tried to kidnapp the young king, to raise him under their influance rather than the one of his mother. OTL, the conspiracy was discovered before it happened, so the guise were exiled from court for a time, but nothing was said overtly. Now, suppose that the conspiracy had gone and the king being kidnapped, only to be released by an attack on his captors ( maybe by a loyal protestant lord? ). The backlash against the League would have to be public and extreme. It could well be to make protestantism the court religion. At this time, the sides were still fluid enougth that this would likely have tipped the scales for the whole of France.
+ As a third, and less interesting possibility, go back to the very beginning. If the 'affaire des placards' does not occur, Francois I isn't angry with protestantism and his sister is still protecting protestants and presenting them. Given the problems Francois had with the various popes, a solution comes immediately to mind...