Let me start by saying that chocolate making is not something that is a very common past time even for us Swiss people (at least not if you are talking making chocolate from scratch). Nevertheless I think you have several options here. Those will also mostly depend on whether your wife is fluent either in French or German:
Cooking courses for local people
This would definitely be the cheapest option with two big caveats: It's probably going to be taught in one of the national languages and it might not be at the level you are wishing for. If you are however interested in this, you can have a look at the Migros Club Schools which are located everywhere throughout the country. You can have a look under their culinary section by searching for a term like "Schokolade" or "chocolat" depending on your language preference. I could find quite a couple of courses.
Cooking seminars offered as activity for groups
This option is usually offered for company outings. While this includes the touristy ones such as Cailler etc, there seems to be some smaller confectionery shops or factories which offer such courses (Have a look at this, this or this). While this is mainly for groups, it should be possible to book the event for just your wife if you are willing to pay. Again, they might only speak German, but you can always email them and ask them if they have someone who can teach you in English.
Courses for gastronomic professionals
There is of course also a whole range of courses directly aimed at cooking professionals. I am not one of those, so I cannot vouch for the quality of such offers. There seems to be a chocolate academy which incidentally also offers English courses in a range of countries and even courses in Brazil. The courses in Switzerland seem to be either in German or French (you can switch language and country with the button on the upper right corner). There is also a Chocolatier School. On the high end there is even a one-year Certificate in Swiss Pastry and Chocolate Arts including a paid internship, however the fees are very high (40k CHF).
Now you might wonder how do Swiss people who do this for a living get to learn their trade. The most common way is to do an apprenticeship at a confectionery shop or bakery. This is either a 2-year or a 3-year vocational education including both on the job training and school training. This is free and is even paid (at a rather minimal salary). While this is usually done after secondary school, this is also accessible to adults.