The number of worshippers is not necessarily countable: the polytheism of the Realms is such that people venerate many members of the pantheon. You might have a patron deity, but you might still pray to another on particular occasions. Quoting from the 2e sourcebook Faiths & Avatars (F&A):
What matters to a particular Realms power is not that a follower worships someone else - most everyone in the Realms worships several someone elses - but rather which other powers are venerated and which are appeased, and how serious a person's offerings and worship are to other deities.
Hence an inquisition like the one you describe in your question does not sound very likely on Faerûn.
Moreover, many powers are allied. For example, Mystra has Velsharoon, Azuth and Savras serving her. Deneir, Gond, Lliira and Milil serve Oghma, etc. Hence an alliance of greater gods against the lesser ones again seems unlikely. Actually, F&A also provides a rough answer to the following question: Given that the power of the deities come from their followers, why do the greater gods let the lesser ones live? (1) Greater powers protect them against other greater powers; (2) Weaker deities pay some amount of divine power to the greater deities, willingly or through extortion. So again, it is unlikely that the greater deities would gang up against the lesser ones.
But if we leave aside the motivation for your question, and focus on the power of each deity from a pure mechanical point of view (as power correlates strongly with the collective amount of worship received), there is one source that provides the information you are asking for: 3e sourcebook Faiths & Pantheons (F&P). Beyond the demi-lesser-intermediate-greater categorisation that appears in most editions of D&D, this book also defines a "divine rank, which is similar to a character's level". While 4e has changed a lot of things about the FR pantheon, 5e appears to be a very strong return to the flavor of 3e FR, with dead or missing deities returning to pretty much to how they were in 3e (or even 2e). So the divine rank from F&P should give you an idea.
According to F&P, a divine rank of 21+ is only for an overdeity (like Ao), and such deities are not interested in mortal affairs. So the "big" guys are the greater powers, with divine ranks in the range 16–20. Quoting F&P, greater deities "have millions of mortal worshipers", whereas the intermediate ones "have hundreds of thousands". (I assume this is again not an ordinary count, but a collective effective measure.) I list below the divine ranks of greater deities from F&P:
Rank 20: —
Rank 19: Chauntea
Rank 18: Mystra, Shar, Silvanus, Tyr
Rank 17: Bane, Cyric, Kossuth, Lathander, Tempus
Rank 16: Kelemvor, Oghma, Sune, Talos
Note: The divine rank for a few greater deities is not listed: Akadi, Grumbar, Istishia, and Ubtao. The first three of these can be considered similar to (or weaker than) Kossuth, as they are all elemental powers. Ubtao's faith is strong only around Chult.
Reading through the deity descriptions in Sword Coast Adventurer's Guide, the power level differences appear to be less pronounced compared to earlier editions. But one can perceive similar power structures amongst the deities. For example, Deneir and Milil are said to be "sometimes thought of as being in service to Oghma". So you might perhaps want to slightly modify the list above, but overall I hope the list provides enough insight to finding the answer to your question.
Make clerics interesting!
There are multiple ways of doing that. The first is to actually play a cleric, they are amazing, they are one of the strongest classes in the game and the most versatile after druids and wizards (Personally, I consider clerics more versatile than wizards, but that's me). I also had strong (bad) opinions on clerics, but then I played a few of them. And damn, what a blast I had, they are extremely fun and you can explore all sort of weird concepts with them, other than your typical healbot or cleric-necromancer.
The second is to introduce them to interesting deities, one at a time. If you find a certain god to be interesting, then maybe they will do too, but without reading about them, how will they know about it?
For instance, did you know the priests (and inquisitors) of Asmodeus (a lawful evil deity) are allowed to act as judges when there is no appointed judge for that city? Not only that, but you can roleplay characters with characteristics like of the Judge Dredd comic (and movie) character, and that is fine, because your word is the law (quite literally sometimes)!
Another example, churches of Abadar are banks! I kid you not, all of their temples are some sort of financial institute. They control the coinage, exchange rates and will give you credit to start your own business for a small fee if you prove that you are capable of doing it. I GMed a game where the players had to constantly deal with clerics of Abadar and one of them was converted to the faith so he could safely exchange trade goods with no risk of being called a cheater, as he had a badge (holy symbol) to prove that he was a reliable source of monetary information and knowledge.
Did you know that temples of Calistria are brothels, inns, and such? So, the next time the PCs wish to get some company, introduce them to the priestess of Calistria, and explain how their donations are being put to a good cause, like saving orphans from a war on a nearby country.
In another game, the church of Pharasma was so well connected to the PCs, both because they did many quests to help the church and because they donated a lot of recovered lost relics (cough archeologically stolen artifacts), that the church would cast any divine spells that they required, and that had a total material cost of 100 gp or less, for free! They used this to cast a bunch of divinations to guide themselves to their goal in that campaign. One of the players even talked to Pharasma herself (when he died, of course) because of this connection.
In that same campaign, they were saved by a monk/cleric of Irori, who defended them against a small horde of ghouls so they could escape safely. Being immune to diseases, he couldn't be affected by the ghoul's paralysis, and being a little higher level than the PCs, he displayed some awesome kung fu action in front of them by taking down single-handledly 12 ghouls and coming back later to tell the story. They had to escape before the combat was over, as 2 PCs were unconscious and paralyzed already. This NPC later became a valuable source of information (Irori is a god of knowledge after all) and allowed them to retrain most feats (a house rule, of course, but Irori is also a god of inner strength) when necessary. They loved Irori ever since.
One last example, in a campaign set in Osirion (which is an Egyptian-themed region), one player wanted to be a cleric of Sobek (the crocodile god) because of the domains associated with him (strength and war), but since we had so little information about that god in the setting and the choice of domains were pretty much for their crunch alone, the god was uninspiring to him once he had finished it. We sat down and looked up everything we could about the (real) god in the (real) Egyptian mythology. And we found out that he also had a strong association with blood (because the Egyptian believed that blood and water were connected) and we pretty much rebuilt the god around the whole "god of strength, water and blood sacrifices".
The result was epic, his Divinations used a crocodile heart as reagents (a flavor created by us), and every blessing involved dripping some blood on his teammates (mostly his own) while chanting some battle cry, while all of his curses involved either turning his own blood into a magical effect, or that of his enemies. Yeah, you read that right, it was all like the Kali-Ma priest from Indiana Jones. He would put his hand on a wound and splash it on his face before casting a Cure Wounds spell while chanting something like "Sobek accepts your sacrifice!" or "Your blood is not worthy!" before a Flame Strike.
As GM, ever since I got my hands in the Inner Sea Gods, I try to introduce a reliable NPC that can instill the awesomeness of their god to the PCs, like those examples above, on every campaign. Those NPCs don't have to be higher level, they just have to do something cool or useful to the party, even if that is simply being a barkeeper that worships Cayden and can turn water into beer for free to the PCs.
All of these examples applies to Golarion, but the spirit in my words go for any campaign setting of your liking. Read up about the gods in that setting, see what makes them interesting other than their powers and spheres of influence, what other gods are their allies or enemies, it's the little details that make them memorable. If your players can identify themselves and feel conneceted to those gods, they may consider worshipping them the next time you guys create new characters.
There is Karsakim. He is the leader of a military force dedicated to eradicating religion in Rahadoum.
Apart from that pathfinder has some abilities that require you to not follow a god.
One example is the feat godless healing
Beside the above mentioned Rahadoum in Garund there are Touvette in the River Kingdoms and Bachuan in Tian Xia that discourage or forbid religious practice.