But by the time people are killing each other over it, 20% of Frenchmen are not going to convert, by force of arms or force of persuasion, 80% of French people, especially with the Spanish always ready to pump funds and troops into the Catholic faction. Despite the fact that the Protestants militarily won the Wars of Religion (1562-1598), their leader Henri of Navarre famously decided "Paris is worth a Mass" and converted, thus ending the squabbles until 1685, except for the occasional Protestant revolts that broke out every generation or so in between. Here's how bad the Wars of Religion were -- they may have killed a quarter of France. Add the plagues, famines, and werewolf attacks, and it's almost a dress rehearsal for the Thirty Years' War down the road forty years.
Can we short-circuit all that misery? Maybe -- if the Huguenots can detach their quarter or so of France's territory, add it to Navarre, and hold off all comers. The Huguenots were strongest in Aquitaine, pushing their fortified holdings to the Loire River and deep into Toulouse. (They were also strong in the Cevennes and out to Grenoble, but nothing's going to let them keep ahold of territory that's been French royal property on and off since the Capets.) This triggers another long war against Spain, and probably makes the hyper-Catholic Guises the Kings of France as opposed to the crypto-Huguenot Bourbons.
Maybe a better English performance against Joan of Arc lets Aquitaine stay under the English crown until 1558, when the Guises capture it (as they did Calais in OTL) for France -- only to see Coligny take it (only somewhat better than his OTL performance, when he co-ordinated a near-simultaneous seizure of most of the Loire Valley with the Prince de Condé) all for Calvinism. Maybe they make the abducted Francis II their King of Aquitaine (a plot that miscarried in OTL), maybe they elevate the Condé to Prince of Aquitaine. The point is to reorient the Huguenots to defending territory as opposed to a war of cities and detached garrisons. This is more than slightly snarled by the fact that the Huguenot Henri of Navarre actually has the only valid claim to the French throne, and would certainly have pressed it. Maybe he gets a salutary defeat at Ivry and must slink back to Aquitaine, tossing over his shoulder some sour-grapes bon mot to the effect that "Paris is hardly worth a Mass." This is likely when the Guises make Charles of Guise king of France outright, assuming Henri of Guise hasn't assumed the throne in a coup in 1588 (aborted in OTL by the decisive action of Henri III).
Although the consequences for the next eighty years or so are dire, they're not quite as dire as OTL -- the Spanish/Guise forces can't necessarily destroy Henri of Navarre, because they couldn't historically, and the Spanish have another running sore in the Netherlands to deal with. Aquitaine catches some breaks when the Guises have to deal with the Fronde and the Swedish in the 1640s. It catches more and more breaks as its economy -- based in textiles, shipping, trade, and coal -- more closely resembles (and no doubt cross-pollinates with) fellow-Protestant England's century-long climb to industrial takeoff.
Maybe England helps out with naval support, although the Huguenots had a major naval tradition (Admiral Coligny was a key Huguenot leader). Which leads me to the strong possibility that Huguenot Aquitaine takes a much more aggressive stance on American colonization than OTL's France. This was a major Huguenot priority from the earliest times (in OTL the Huguenots tried planting colonies covertly in Brazil and Florida), and was partly why the French monarchy refused to allow mass colonization. Perhaps all the Huguenots expelled from the Lyonnais head to French Carolina, or the Huguenot fleet (along with Grenville or Hawkins or someone from England) captures Quebec during the final stage of the war and they flood into Ohio afterward, right around when the Iroquois Confederacy is forming.
I think I'll leave it there, with a big, Protestant, French-speaking colony (Nouvelle-Aquitaine) slowly melding with the Iroquois (unlike OTL, in which the French supported all the surrounding nations against the expanding Iroquois -- but settlers intending to farm instead of rake off beaver pelts would rather placate the Iroquois than not). We'll even leave an English enclave from Virginia north to Maine, east of the Appalachians. England and France (expanded into the Rhineland, maybe) are looking to square off in Europe and overseas. Aquitaine and Spain are likely going to be dragged along, or maybe their endless squabbling over Navarre starts the next round of wars. Feel free to blow up this 18th century in comments.