Possible solution to protect smaller guilds could be the following:
Attack time windows:
(Attack time window = is time when your tower can be attacked)
A small guild (20 members) could set ,a s an example, its attack time window on Saturday from 20 GMT to 22 GMT.
(20 members is minimum 2 hours attack time window)
While a big guild will be forced to set a bigger minimum attack time window.
For instance a big guild will be forced to set mabey multiple attack time windows.
You could either set a minimum attack time window with also lesser bonusses or a max window (24/7) with max guild bonusses.
The minimum attack time window should be linked to the number of members of your guild.
This avoids guilds to up their numbers by members having six alts.
cuz this would actually penalise these guilds by being forced to set a large attack time window.
Also these attack time window make it possible for guilds to be able to defend their structures at a conviniant time and could solve the problem of different time zones in the favour of the defenders.