It does not matter what you do with the water. The flatulence has to do with the high amount of dietary fibre in legumes. If your digestive system is not used to that dietary fibre it will lead to spectucular gas.
I have been on a mainly vegan diet for close to three years now. I have eaten lots of lentils, beans and peas. The flatulence platues as your body gets used to it but it has not really gone away.
I personally use the juices as you would vegetable stock. A lot of the nutrients of canned vegetables goes into the liquid.
There is never really enough to use it instead of stock but there is no reason not to use it with stock.
Even if my view is just based on my frugal middle class upbringing where I was taught not to waste any food.
You should consider the fact that the more effect sudden fibre consumption has on your digestion. The more you need to continue eating that food
Regular bouts of flatulence is a sign of good health. Regardless of what minor embarrasments it may cause.