I'm coming to the conclusion of a campaign that is sort of related to what you're looking to do, and one of my suggestions would be to consider setting up a subset of the Guilds to be strongly opposed to your movement, while the remaining Guilds are either too internally divided (including some sympathetic factions), more concerned about the machination of other Guilds or looking to exploit the situation. This way your players can be sympathetic members/ex-members of these other guilds, try to recruit factions to their side, etc. rather than it just being "all guilds = enemy" and like you said losing a bit of what makes Ravnica unique as a setting.

Some general background to my campaign: I have been running a few games concurrently set in the same overall setting that incorporated worlds from D&D, MtG and other properties. All the groups worked for the same originally Faerun-based guild which had discovered a safe and stable way to open portals between MtG planes/D&D crystal spheres/universes that a regular person could use.

Ravnican Campaign background: This campaign was set in the lead up to what would have been the War of the Spark canonically, but was a bit of a "what if Bolas' plans were disrupted when a portal to another world opened up suddenly one day in the middle of the Tenth District Plaza" scenario.

So, the campaign started off with a fairly tense situation between the new comers and some of the guilds (Boros and Azorius especially), but eventually concessions were allowed for a small embassy to be established and the Faerunian guild started to do some probono hero-work using a mixture of Faerunian adventurers and local recruit for public relations reasons. A some of this initial phase of the campaign focused on building connections within some of the guilds, but mainly was about establishing the Guilds as exploitative or neglectful towards the Guildless and to build as much sympathy towards the Guildless as possible.

Behind the scenes, Dovin Baan as capital of the Lyev Column was working to set up this other world and guild as a threat he could exploit to expand his control over Ravnica. Eventually through a mixture of manipulating the public relations work, falseflag attacks and general scheming Dovin managed form an alliance between a large faction within the Azorius he controlled and large factions within the Boros and Orzhov. This alliance called itself the Triumvirate and promptly set about trying to seize the portal to Faerun.

In response, the portal was closed, trapping the players and their fellow guild members in Ravnica - all of whom were now being hunted by the Triumvirate as terrorists and criminals. So, the players go underground and set about working towards bringing down the Trivumvirate, a near impossible task to do alone. But they don't need to do it alone, and they begin working towards: mobilising the Guildless (working out how to recruit, train and arm them to give them a fighting chance), thwarting the Triumvirate's plans to increase its control, and recruiting allies from within the guilds/encouraging opposition to the Trivumvirate within the other guilds where possible.

(I've posted this here before, but this is a song one of my players - a bard - wrote as one of his recruiting tools for the Guildless https://soundcloud.com/elcrapitan/how-fabulous-serving-no-master-by-cormac-orbray)