Does this not mess up bussing? Does an assistant watch them for those 15 minutes? Do they go to another class? Is it affecting your pick up or drop off time?
If it affects your pick-up or drop off times - I would definately complain. People have lives....and one persons scheduel should not dictate everyone elses!
If it does not affect your scheduel it still might bug me.
The word
might comes into play because it would depend on how the school behaves in other circumstances.
Are they generally a flexible place? What do you think would happen if you tried to take your child out of school 15 minutes every day? Would they accomodate that with a smile?
I ask because I

flexible work places. I find it very family friendly. If this flexibility is also extended to you, I see it as a good thing. If it is not extendede to students and familes, I would be really annoyed.
I would not worry one iota about 15 minutes of lost academic work a day. I believe a good 1/2 (if not higher) amount of time is wasted in school everyday due to attendance, discipline, lining up, etc. 15 minutes in not a big deal. Moreover, if there is an EA, I imagine she will be simply following the teacher's plans anyways.
Even though I would not worry about the academic issues, I would probably end up writing a note. It shows a lack of concern for students, IMHO. Quite frankly, nothing galls me more than lack of concern. The only exception would be if this were known as a family friendly, flexible school - in which case I would be Ok with it (as I like these values, and knew this school was "accomodating" up front)
I hope this makes sense. It seems a bit garbled. In any event, kudos to you for writing a letter. You are not the "crazy mom who does not let anything slide" (an idea
meant to keep people compliant and apathetic) - speaking up about your DC education is your responsibility.