Well I am not sure the exact timer on prayer, but didn’t pray have like a 5 min cooldown or something to that effect and then it lasted for 2 minutes? something like that. I am thinking the bonus only lasts for the duration of the prayer, and the inherent 5 min cooldown should keep it balanced, but then you can kind of switch prayers as needed during a hunt and its already got cooldowns to to keep it in check.
I would probably be against prayers overlapping that would probably be too strong so the perks should just last the duration of prayer. I was thinking that the perks would just last for the duration of the prayer uptime, not linger. To increase paladins power as you tier up tho, you could change the duration of pray and make it more like berserk, so that as you increase in tier, the longer your pray stays active. I think you started with pray in original Nexus but you could make it their level 10 ability, and then have it start at 1:30 seconds active duration on a 5 min cooldown, and have it increase about 10 seconds per level. Those numbers subject to tinkering if the cooldown was longer, I am not sure what it was.
That said you could still have a follower aspect, so that whatever god your following increases the effectiveness when you pray to them. But generally you would think a religious character would believe in the other gods as well if they are following one, so I think it would make fine RP sense to be able to pray to the others, but you would just receive baseline blessings from the one you weren’t following and a nicer bonus from the one you were following.
You could also do something like you said, lets say you follow Erisar and pray to Dilanis. Maybe it gives you a partial damage increase from Erisar as well as the bonus healing from Dilanis, since you follow Erisar you get a small bonus from him whenever you pray. Then if you pray to Erisar you get a damage bonus for praying to him, plus your follower bonus so it increases your damage more significantly. So yea pray might give you X bonus and following gives you Y bonus and they both activate when you pray.