I really don't see the point in removing guild ranks.
If you are the top elder... you won't be replaced anyways. Guilds don't replace missing members. They only do so when there are no elders left, and even then they don't give #1 spot. If paused characters count against the limits and prevent this from taking place... then just change that, instead of changing how pausing works.
Dwilight is big. Makes no sense to force players that have joined guilds from a bit all over to have to travel it all again if they need to leave for 4 weeks.
Also, some religions already work without their founded. Verdis Elementum, for example. Now, if the elder of Fire uses cold storage, it's gonna mean we'll never again be able to put someone in the top 4 elder ranks or so. Just because the guy paused. If I hadn't had the rank just below, it could have easily meant that instantly the top 8 elder ranks or so would have become permanently inaccessible. And whenever the guy would have come back, there'd have been no way to give him back his rank. Nor give it to anyone else.
The feature makes no sense and screws over religions and guilds more than anything.
I already scrapped a guild and a religion because of this feature.