Now let me begin by saying I would like responses in RP form if you could. The situation is this, my character has been named Arch Mage of the College of Winterhold and has spent the better part of the first month in this position attemtping to rebuild the relationship between the people of Winterhold and the College. I have done enough that the Jarl has named me Thane but his attitude toward the college is unchanged. During all of this the civil war is raging. While I am attempting to keep the College out of the war I am now torn because I can see entering the war being of benefit to the college.

On the one hand I feel that if we enter the war on the side of the Stormcloaks, we have the chance to help our relationship with the Nords. However based on my efforts to date within Winterhold I am not sure that even aiding in the war will be enough to turn the people of Winterhold to the College or overcome the distrust of magic Nords have.

My second option is to put the college resoruces into the hands of the Empire. They have always been very supportive of Mages and a victory by the Empire could mean a new Jarl in Winterhold that would be supportive of the College. My issue here is that the Thalmor have already atemmpted to have me killed once and I am concerned that siding with the Empire might be wrong do to the current position in regrards to the Thalmor.

To this end I seek the advice of the wise mages of the College to help me lead the College onlong a path that will be a benefit to mages in Skyrim.

Please guys, no spoilers just thought it could be an interesting discussion

My mage had the same issue. He ended up joining the stormcloaks. He had a 'deep deep' hatred of the Thalmor. I RPed that he went to Ulfric, and offered the help of the college, but on the condition that within the new free skyrim the college would be treated as its own hold separate from Winterhold.... The college of course could afford to pay an entire hold's worth of taxes by supplying the stormcloaks with enchanted weapons and of course a whole lot of gold(the transmutate spell).

I wouldn't think that siding with the Empire would develop more tensions with the Thalmor. If they weren't able to kill you with the Eye of Magnus they won't be able to in many other subtle ways where killing you would just create very bad relations between them and the Empire. However, I would acknowledge that the Synod might want to combine with the College of Winterhold. This could be bad for you since it could terminate your rank within the college, but Winterhold could greatly benefit from an influx of mages which could, in time, make the entire town a mage village.

To side with the Empire after their attempts on your life sends a clear message: "I am afraid and I bow to your will."

Don't be a puppet trembling on your master's strings. Kill the Imperial scum and then use their corpses to kill their own.

Death is just the beginning.

this post contains College of Winterhold SPOILERS!

Jerian sided with the Empire long before he became the Arch-Mage, and it benefitted the College enormously. The new Jarl is a friend of the College and is close friends with the new Arch-Mage, and the Thalmor have no presence within Winterhold.
he sent a clear message to the Aldmeri Dominion - the Thalmor have no right to enter the College, and will never be given such rights.