There are clearly two separate issues here.
1) What to do about the draft: Should you register and get a ‘dichui’, or should you not register at all.
2) Is there something wrong with protesting in the streets.
Those of you who think it is a Chillul Hashem – do you think it is a Chillul Hashem because you disagree with R’ Shmuel Aurebach’s position, or do you think that the idea of protesting (causing traffic, disrupting medical services, causing people to miss flights) is wrong? If the answer is the latter, you would be upset regardless what they are protesting about. If the answer is the former, then you don’t have anything against the medium of protesting, but you don’t think there is anything to protest about.