Religious tolerance wouldn't have been an alien idea to Europe at the time. Erasmus was a famed Dutch humanist who urged religious toleration, and he died in 1536, some 26 years before the start of the French Wars of Religion. Pope Clement VI had suggested tolerance of the Jews in 1348, and would even try to protect Jews at his residence in Avignon, but that whole tolerance thing really didn't spread. The Kingdom of Poland and eventually the Polish-Lithuanian Commonwealth were both tolerant of Jews, although that's not the same thing as tolerating Protestants. Some reformers like Zwingli were intolerant of other creeds, and some reformers, like Luther, were alright with just expelling those of different creeds except in cases like the Anabaptists, who caused political trouble by doing things like refusing to serve in the military. Some reformers didn't agree with the Anabaptists, but didn't want to see them get murdered. Sebastian Castellio was a French theologian who also urged religious tolerance, saying that people can only live together peacefully when they control their intolerance.

On a state level, the Edict of Torda in Hungary and the Warsaw Confederation in Poland-Lithuania were both national efforts to urge tolerance. France actually had a limited act of religious tolerance before the war began, in the Edict of Saint-Germain, which proposed limited religious toleration, but wasn't really put into practice and fell apart as the Wars of Religion began in earnest later that year. The war was ended with the Edict of Nantes, which was a bit more effective, although not great. Catholics were angry at official recognition of Protestants, Protestants wanted parity with Catholics. The Edict was signed by Henry of Navarre, who was Protestant before ascending to the throne and converted basically just to secure his royal power. Catholicism was still very much the French state religion, and Huguenot revolts would break out later in the 1620s.

I think toleration was an idea to an extent, but "full-throated pluralism" was very rarely one. Western Europe was used to the monopoly of the former Latin Church (predecessor of the Catholic church) and religious suppression had a long history before the reformation, although the confessional division certainly inflamed it to new levels. Toleration was often promoted, in my reading which is admittedly more in England, on the grounds of general moral qualms (try not to kill too many people) and pragmatism (we can't actually force people to convert) and therein was often a limited toleration. Erasmus didn't advocate full equality or pluralism but merely "it is better to cure a sick man than to kill him". The Edict of Nantes mentioned already was one of the more dramatic examples that came closer to full equality but as mentioned it was not quite equal, and did not last because Catholic French kings came in and increased persecution of Protestants.

I've never heard of anyone advocating a modern kind of liberal secular pluralism or anything particularly close to it, which is an idea connected to liberal political philosophy in the 17th-18th centuries and the aftermath of the Thirty Years War. At the time in Late Medieval and Early Modern Europe before that, it was generally considered obvious that divergent religion was sinful and politically disruptive; a radical element that promoted unrest. If you really do believe that heterodoxy and alternate religions are sinful then it makes sense to seriously oppose them. "Curing sickness" as Erasmus put it, it was rarely treated as good or okay for there to be religious disagreement which was frightening to people. It's quite possible at some point some people considered genuine pluralism, but I haven't seen anyone who was willing to put it to words or enact it.