Like the reactions of Jews did years ago?
I see this as going one of two ways - Switzerland will start banning burkhas, object to prayer timings, object to social activities of Muslims and eventually do what Europeans always do when faced with another religion or culture. Have a nice little pogrom. They've already started vandalising the mosques so that seems like the most likely route. Only 4 minarets and 5% of Muslims make them feel threatened enough to get there, a more visible Muslim population will drive them berserk.
The second, the ECHR will exert its influence and there will be a shift in how direct democracy works in Switzerland, with people becoming limited in their ability to choose what they can vote on. This is the less likely option
Either way, they will blame the Muslims for spoiling Brand Suisse. If I were a Swiss Muslim, I would be looking for alternatives to Switzerland. Better safe than sorry.