I have two answers for this question.
Yes, now: Well roleplayed guilds that hold true to the Settings should be rewarded. Simple things like being given guildhouses, mention in books and by NPCs, and perhaps approved and supported guild submitted textures for uniforms. At this time, I would grant no actual powers. However...
Yes, eventually. Eventually, true approved guilds should be given vast powers. The guild system in place is too simple to handle True Guilds. Look up guilds historically to see what I mean by 'true'. 'Guilds' in games are nothing more than big clubs for the most part, and most can barely be trusted to name themselves, let alone give them power over anything.
What kind of guilds would I approve for having ingame powers? True trade guilds only (yes, that includes the 'evil' trades). Other things such as political and religious organizations would also be able to obtain powers, but under a different way, since you can be a part of a Trade guild and both of those as well.
Restrictions: With great power comes... many rules. Approved guilds would become property of the Settings department and a tool for them to use, just like NPCs. Settings would reserve the right to advise and force changes in the guild, as well as edit its history. Trade guilds with powers would have even greater hurdles having to establish from the beginning what their intentions are, what trade they will be taking, getting their history approved before starting the guild, AND actually having to be a master in the trade that their guild will be focusing on. Trade guilds would also be restricted in what they can do and where they can practice their trade. People who get into a trade guild and advance to a certain rank would NOT be able to leave until a certain time passed. Characters would not be able to practice their trade outside of their guild's territory.
What sort of powers would guilds get? Certain ranks of Trade guilds would be able to get the materials and training needed to advance in their trade from NPCs at very reduced costs. Trade guilds could own and restrict access to such things as mines and other sources of raw goods, industry facilities, operating areas, and flying beasts (no other type of guild could own one). They could also affect the prices, quantity, and quality NPCs would buy and sell by bringing the NPC into their guild (based on Settings approval). Laws could also be affected by guilds, making them more or less lax.
As for the 'favoritism' counterpoints? Honestly, boo hoo, cry me a river. Anyone who can get their guild approved by Settings deserves to be favored.