The same way Stoner SHOULD have shaken Rossi's hand after Laguna 2008 - it is called graciousness in defeat and is also known as 'being a good sport'.
Failure to shake hands or acknowledge after a sporting event, no matter the circumstances or consequences reflects on the person who fails to make the effort, and it reflects poorly.
MM is yet to take another rider out or make them fall in his MGP career (from memory) so here goes.
Simoncelli - well documented
Barbera - as above
Bautista - crashed took many riders out over time
Rudroff (well before your time) - slow, like really slow and would meander on or off the racing line
Chili - was a bit of a rat at times
There are more ..............
MM is and has been quite safe in his MGP tenure by comparison to many other riders, so please do keep digging.
Oh, and before you start, VR has also been relatively safe during his MGP tenure, particularly when you look at it as a 'per race' basis but like others, he has had his moments (although from the top of the head, I believe that MM may be the first rider that VR has caused to crash as opposed to just running them wide etc as he did with Gibbers, Lorenzo and CS amongst others)