Hopefully this reaction will pass in a couple of days, some people seem to have it as Cath mentioned, even those without an autoimmune disease.
I have read a lot about flu shots for Lupus patients from many different sources. The advice is that it is safe for most as long as it's the injectible form not the nasal spray one. This advice is as long as you are not seriously allergic to eggs. One source say the vaccine is less effective in Lupus patients taking Imuran but that was based on a small study of 56 patients, a host of other sources says that is is advised to have the shot esp if you are on Imuran. If in doubt the best person to ask is your Rheumy as he knows your individual circumstances and should be up to date with current thinking.