We've seen both leaders getting Tempered by Primals and the Twelve being summoned. Nael is what happened when Bahamut tempered a Legatus (and Bahamut has the most terrifying version of tempering we've seen yet). The Twelve were what Loiusoix essentially summoned to try to keep Bahamut back... and they failed! And then all of Eorzea summoned the Phoenix which got tempered by Bahamut... So whatever Eorzeans think of their gods... their manifestations are weaker then Bahamut. Which isn't saying much. That's probably true of all the primals we've met except maybe the Warring Triad.

As far as I can tell, the Eorzeans are not against religious observations by the beats tribes. Just the various religious sects which summon primals which often times are the people in power over the majority of the beast tribe. Both the Vanu Vanu, the Sylphs and the Ananta (and probably the Kojin) worship the same deities no matter if they summon them or not. It's just that one faction of the tribe thinks that the primal version of their diety is a false or wrong version of the god(dess) and refuse to think their gods would not let them chose to worship them. Heck, Rahmu flat out refuses to temper slyphs unless they actually want him to temper them or not. And for that matter, we've actually seen about as many primals who haven't tempered people on-screen as those that have. And the degrees of tempering varies a lot between primals; Ifrit's and Leviathon's are super obvious, Bahamut's tempering of Nael was never noticed.

As for dealing with summoned primals without the WoL... this is what people did from the time Midgaurdsormr downed the Agrius until 1.0 started (and even a little after that, so... 15 years or so?). It's not that it can't be done, it's that the casualty rate is crazy high.