Let's say a magus has a familiar who murders another magus without the benefit of Wizard War then destroys said magus lab ?? The Magus who's famil;iar did the deed claims that their familiar did the deed and he did it without their action....
Would the Magus who's familiar did the crime be guilty for the acts of their familiar..??
Or would the Familiar be held guilty..??
Or Both..??
Thrumbar 
This depends somewhat on the tribunal, but most likely the magus will be held acountable for his familiars actions.
I would think the Magus is responsible for his familiar's actions in the same that he is responsible for his aprentice's actions.
Although it might be a bit a bit harsh to march the said magus even though he is technically responsible/guilty for/of the murder. In my opinion an appropriate sentence at tribunal would be the death of the familiar.
Hail Eris!
Flarg
Tricky.
I would hold the magus accountable, definitely. But not of a High Crime unless I have a good reason to suspect the magus is using his familiar to get away with murder.
Death of the familiar is a reasonable penalty. If I'm at the Rhine or Alps tribunal, I'll add also exile for an alloted period of year.
Fines payed to victim's lineage and covenant are also to be considered. Killing another magus is the greatest offence possible, and the punishment must be so severe that no one in his right mind would want even his most qurrelsome familiar to kill even his most hated rival. Heavy fines and the "donation" of some of the magi's magical secrets to the victim's filli should put a chill on any desire to settle scores in this way.
Loss of a familiar is a minor punishment... And we are talking about a murder here... I'd say march him, but as with most hermetic trials, it is up to the tribunal in question...
IIRC some opf the older material listed loss of a familiar as the harshest punishment aside from death (second harshest) and loss of the gift (harshest).
I agree that puishment is really up to the tribunal where the case is heard.
Game mechanically, a familiar isn't too hard to replace. In character, though, a familiar iis generally supposed to be as close as a loved spouse or family member, if not closer, and its execution should be a major emotional trauma for the mage.
I'd ax the familiar.
According to the situation you established, the Magus is not guilty of the crime. However I do feel the magus is responsible for the actions of the familiar in the same way he is responsible for the actions of an apprentice.
I think Marching is to severe. Killing the familiar punishes the Magus who is responsible for the familiar and it also punishes the character responsible for the crime. It seems the reasonable solution.
Having said this True Lineages suggests that the Q's loath the idea of taking anything to trial. Every attempt is made to resolve a matter prior to trial. Take into account the politics of the Rhine and then some of the other answers begin to make sense.
Heavy, and I mean Heavy Fines. Banishment.
There is what's suppose to occur and there is what occurs and in between is what you would like to happen. As a storytelling game, what interests you most?
If the familiar is an actual character it may be to severe to kill it without ticking off a player. On the other hand killing a troublemaker character may teach a player there are limits to what they can get away with. Hermetic Murder isn't one of them.
I like the notion of banishment. It's unlikely a banished magus would have access to labs or resources for a while. This is an easy way to limit their growth. While a player may not like that, the GM might as player power issues seems to be a reoccuring problem in various games.
Beyond that, storywise banishment sounds cool. One can leave the politics and world they've established and tour Mythic Europe. Walk the Earth like Kung Fu, or better yet, show up at your Pater's door and say, "Hey Dad, I'm home!"
I think the punishement, in addition to clarifing the limits of bad behavior should be seen as storytelling starting point. So what sort of story telling do you want to pursue?