I don't think mine will start with the side stand down and bike in gear, even if i have the clutch pulled in. Although I can't think of a situation when I would have tried it.
It starts ok in gear with clutch pulled in if the side-stand is up. And it definitely cuts out if i put it into first with the sidestand down (even before i release the clutch).
I had assumed this is all by design and don't have any problem with it.
I've heard stories of people disabling side stand switches quite easily if they were bothered by this kind of feature. On the other hand, I've also heard stories of horrific accidents when people accidentally rode off with side-stand still down.