I wouldn't call the Prime Minister calling for a pardon 'part of the process' - it is quite extraordinary. As far as I understand it, the soldier (Azaria) was found guilty by a military court, but the President has the authority to issue pardons - and so supporters of Azaria, which includes the Israeli Prime Minister and other top ranking politicians, are calling on the President to over-rule the authority of the military court and quash the conviction. But, ironically, by seeking to overturn the conviction via a Presidential pardon (as opposed to an appeal and possible retrial), supporters of Azaria are only likely to undermine the authority of the military - which seems incredibly self-defeating.
I'm not sure I'm getting what you are saying here... if the sentence is commensurate with the act (and is not unduly lenient), then that would indeed signal that the 'process' works and that no one is above the law. But, if that sentence is subsequently commuted/overturned by a Presidential pardon, that would clearly send out the opposite signal i.e. that IDF soldiers who are found guilty of manslaughter will not be punished.