I find there are contradictions in your post. You mention that there are guilds with only a few members in it, but you want to take away one of the many reasons to join a guild. This would result in just another reason to not join a guild. Guilds offer many benefits outside of towers, and are one of the better parts of this game and, as said above, one of the main features of most MMORPGs. A healthy Runes of Magic for the entire population means there are numerous active guilds, imo.
if people want to have access to guild benefits, they should join a guild. I see several guilds advertising in world chat every day recruiting any level, so it shouldn't be hard to find one.
Also if a guild no longer has an active leader, they can write a ticket to support if the leader has been inactive/not logged on for 90 days (I think?) to get the leadership transferred the highest rank that is active (I did this a few months ago, and it takes until the next maintenance and you need three ranks in chat to agree with the transfer, unless there are no active ranks).