I had this same problem during a visit to Geneve last week, and solved it at the Cafe du Soleil, Place du Petit-Saconnex, where I had a great fondue on my own.
I would recommend this restaurant to anyone, whether or not you are travelling alone. It is in the suburbs, so although it does get a lot of visitors many of its customers are locals. It definitely feels like a local neighborhood restaurant, and is friendly and welcoming. Prices are reasonable by Geneve's high standards.
There are a number of other Swiss dishes, as well as reasonably priced wine with several by the glass or carafe. Its fondue is rated as one of the best by several reviews I read. I think its probably a much better option for local food than the more tourist orientated places in the centre of town.
There is a definite technique to eating the fondue, which I didn't quite get at first. However, one of the locals sat at a neighboring table saw this and came over to show me how to eat it properly !
If you are staying in the centre of town take the number 3 tram from near the railway station, this has a stop directly outside the restaurant.