Make the guilds specific to each country and maybe even specific towns.
Make these guilds compete.
Make it function like a real guild, with apprentices, journeymen, and masters as the ranks instead of some retarded pseudo leveling system dressed as a ranking system.
Make sure the guild is doing jobs that the military actually wouldn't do, like providing muscle for searching ruins, running bodyguards for low level merchants, or doing shady shit for the local wizard. The *insert random noble asshole her* of the area isn't going to pay a bunch of armed thugs to clear out that encampment of raiders/orc or deal with local dragon, he has an army for that shit. If he doesn't why is he even still in power?
If the *insert asshole noble here* does use the guild for hired muscle make it because he needs expendable mercs, or make it so that guild is actually the true power behind the throne.
Make being a murderhobo still a thing, but make it illegal and make sure that everyone treats non-guild adventurers as complete untrustworthy shit.
Make the guild real shitty towards poor people. It's a business not a charity, quests are filled based on how much the quest giver is willing to pay. Your village is being gobbed and you only got 2 pence together as a group to pay for some murderhobos, too bad Mr. Inbred Peasant, Fancylad Mcrichpants over there just paid 100 gold sovereigns to have some adventures beef up security at his fancy dress party.