Namaste Vaibhav,
The one sided aspect of just doing pranayama and the effects of it has been discussed at length in a previous post, I copy the link for you here and think it might help you as well, as there was many valid points mentioned i that post.
http://www.yogaforums.com/forums/f16/pranayama-and-anxiety-3494.html
Hope this also helps you in gaining understanding of your condition.
Now to answer your questions: My own teacher has always warned us against doing unguided and immature pranayama when one suffers from any problems relating to the stomach as well as colon and recommended expert guidance in such cases. If pranayama is prematurely applied without proper pruification through asana and other yoga practices, you might just exacerbate your condition. You might experience short moments of getting better, but because your approach lacks the support and integrity of other related yoga practices, this will be short lived and a host of other problems will start to show themselves.
Please also note that pranayama doesn’t just works on the physical body, but also on the five other doshas as well as on the ida, pingala ansd shushumna nadis. For example, the Breath of fire, which creates heat in the body, counteracts imbalances in vata dosha or the wind element. I think you can already gather that pranayama is not just simple breathing exercises, but something you need proper guidance, especially if you have some medical conditions you want to treat with it. I would recommend that you seek the help and advice of a yoga therapist in your region.
Good luck and I trust this will help you in making future choices.