Guilds should only restrict you by your talents, and NO I don't mean by "your skill X is 2 points too low" but by having you do a initiation test, if you fail you don't get to join.
If replayability is the thing you want have branching quest lines instead so different combinations of guild memberships give you different mission sets AND how you join them differs too. You could for example work as a middle man between two guilds or infiltrate one to sabotage it. Or work secretly for both the same time, for this you'd have to well balance which missions to take so they don't overlap and reveal you.
I like your idea of infiltration and/or secretly working for 2 or more guilds. I just don't like how you can become guild leader for every guild at the same time. I think of it as different "gangs". For instance, you cant become leader of 2 different motorcycle clubs, but you could infiltrate or secretly work for multiples or sabotage others. To expand on that, if you were caught working for multiple guilds you could be removed from 1 or all depending on the negative/positive attention you bring to the respective guilds.
In addition, I think that becoming an all powerful fighter and all powerful mage to lead those guilds is a little too god like. I can see, however, joining and progressing through the thieves guild and assassins guild as members/leaders of the mages or fighters guild. It may need to be a done as a secret though depending on guild alliances and charters.
I would just like to see a more in depth story around guilds and their respective relationships and get one exceptional benefit for becoming leader of a particular guild(i.e. mages guild receives a mages tower with plenty of storage and all you need for alchemy and spell creation and battle mages to guard the tower)