The main disadvantage of alliances between entire kingdoms is the possibility for the game to get boring, with nothing to defend, nothing to attack, nothing to do at all... So the game starts to be a farming game... The advantages are more for previously "opressed" kingdoms, which now can have at least some cities to explore...Pros and cons of this are to be considered by the kings each week, and that is perfectly ok.
Alliances between guilds of diferent kingdoms would be interesting, with similar rules to the alliances between kingdoms, but envolving only the players of the guilds allied. Also, a maximum number of allied guilds is an interesting concept, preventing that all guilds would associate in a single and dominant cluster. Also alliances could be balanced by the power of the guilds involved, so that big guilds are in different sides, stimulating some activity regarding city attacks and etc.
Hope this is a good contribution, cheers!