Alright, so. Got a guy in my group that wants to integrate the Magic School system, more specifically the guilds, from Inner Sea Magic into a game we're playing but I personally feel that it'll just be him benefiting since he's the only arcane spellcaster in the group. My main question is if there's equivalent rules for martial and divine casters as well or am I better off trying to homebrew an equivalent.
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This sounds like a perfect situation to home brew.
Historically, every profession generally had a guild. While the guild system has largely been replaced by the welfare state, trade unions, and national health service, some traces remain to the modern day.
In small towns and villages, where there were not enough people of the same profession to form a guild, 'odd-fellow' guilds were formed by all the people left out of the 'big' guilds (e.g. Masons and Goldsmiths). Several such organizations still exist, albeit in altered form.
The history of guilds on Earth might provide some useful help for brewing your own on Golarion.
Try integrating all the factions instead of just the guilds (see the Faction Guide supplement). Everybody can get boons that way, and it can make for some nice plot hooks and even some dilemmas for characters that don't usually have to worry about codes or ethics.
Rite Publishing has two guides for two particular 'factions', and an idea that could be extrapolated on for other guilds, but Way of the Yakuza has yakuza gang creation rules based on the city stat block (which could easily be adapted to a Thieves Guild). Way of the Samurai includes samurai clan creation rules, also based on the city stat block (which could easily adapt to any noble/cavalier house).
You can review both creation rules on d20pfsrd.com.