Hi C.. I am of your same belief in not overtreating, but in preventing. My daughter is 4 and my son is 2 and we chose to give them their first flu shot ever this year. I stay at home and do not have my kids in day care where they are exposed to many other children. I did enroll them in a once-a-week gymnastics class where there are several children of all ages. With the anticipation of exposure during flu season, we jumped in and did it.
I was especially concerned about the link between certain vaccinations and autism - the jury is still out on that one. To be on the safe side, I read the materials about the flu shot and read that there is thimerisol-free shots. (However after grilling the clinic staff, they say Kaiser hasn't used thimersol in their shots for a few years now.)
My 2y.o. son got one shot, then had to return a month later to get the 2nd shot. My daughter got the nasal-flu nose spray (apparently you can get this after age 3.) Neither had side-effects, other than a low, low-grade fever for a couple days and a little more clingy than usual for the same time. Glad to say, they didn't get the flu!
I hope this helps in making your decision. - KW