I think you are being very sensible in raising concerns re medications prescribed, it worries me to think that most of these new medications have not been on the market for all that long, yes I know stringent tests have to be carried out before new medications are unleashed onto the public but even so, they are chemicals, which means they are toxic to our bodies.
Personally I am scared of any medication nowadays, there was a time when I swallowed several prescribed medicines three times a day, then the side effects started, which meant yet more pills for me, eventually I became very ill. I dont take any medicines now, prescribed or otherwise.
Having said that I know of 2 people who are very happy with Metformin and Januvia, both long term users, it helps them to achive good bg levels, they have not experienced any side effects to speak of.
I'd say keep an eye on things and any problems cropping up dont delay in seeking medical advice, there are other effective medicines your doctor can prescribe if you are nervous about the Januvia.
How is your diet, do you restrict your carbs at all? Reducing carbs is another option to achieve better control.
All the best to you