There's an incident of crowd interference in Quidditch Through the Ages. We learn that the Ministry has used defensive spells to take preventative measures (in league games) against the sort of low-level interference that Hermione undertook.
Refereeing a Quidditch match was once a task for only the bravest witches and wizards. Zacharias Mumps tells us that a Norfolk referee called Cyprian Youdle died during a friendly match between local wizards in 1357. The originator of the curse was never caught but is believed to have been a member of the crowd. While there have been no proven referee slayings since, there have been several incidences of broom-tampering over the centuries, the most dangerous being the transformation of the referee’s broom into a Portkey, so that he or she is whisked away from the match halfway through and turns up months later in the Sahara Desert. The Department of Magical Games and Sports has issued strict guidelines on the security measures relating to players’ brooms and these incidents are now, thankfully, extremely rare.
In short, crowd interference is very rare, presumably quite easy to detect (for an experienced referee) and quite easy to prove once it's taken place.
There are no stated guidelines regarding what would happen if the snitch is meddled with, other than that the referee has a wide leeway to deal with unexpected issues. Presumably it would simply be put back into play or (if physically handled) replaced with a fresh one.