I gave this strategy a little more thought, here's a map to victory for the Thieves guild
1. spread rumors within Windhelm that the high ranking members of the Companions swore secret oaths to Ulfric Stormcloak. This information will be reported to the Empire via Imperial spies within Windhelm.
2. use Thieves within the College to drain their resources (such as stores of food and gold). Start this long before step 1. This will force the College to trade in more resources, which will be shipped using caravans that are controlled by the Thieves guild, meaning that contents, routes, and arrival times will be known long beforehand.
3. hire the Companions to take a large caravan controlled by bandits near Winterhold. While they are on their way, tip the Empire off that Winterhold is about to suffer an attack, and use forged documents within Windhelm that corroborate this, and allow them to be stolen by Imperial spies, to be reported to the Empire.
3.5 as an optional method, you could reverse all of this and lead the Stormcloaks instead, or even lead both forces into Winterhold, either side slaughtering the Companions on the way (due to the Companions attacking the College's supply caravans).
4. lure the Stormcloaks into Winterhold as well. There are any number of ways to do this and you can probably think of one. Kind of like how you lured the Imperials there.
5. The Companions will most likely be slaughtered while attacking the caravans. You may actually use insurgents to create a plan to fill the Caravans with Stormcloak soldiers, possibly as a means to bypass the Imperial army to get into Winterhold, where they can fortify and hold out for a siege.
6. now you have either the Imperials or the Stormcloaks taking and fortifying the College like a fortress to fight the other, either way you destroyed the Companions and the College is completely removed as any form of independant power, with the mages either being taken prisoner or being forced to supplement armed forces.
7. the rest is as easy as controlling the imported supplies for any army on the battlefield. Feed the attacking force lots of supplies, to keep the siege going, and secret in supplies for the defending force to keep them fighting and attaining casualties.
8. Any number of strategies could be used to indirectly win at this point. Disease, mass poison, if you control their supplies you can easily poison or cut them off, halting fighting or forcing it to continue. The options are endless.
