Alright, I was able to solve this on 2 ways. Going to explain both of them here so anyone that finds this thread can do it.
As well please read full post then start doing anything there are many things that you need to decide what are you going to do as well what are your configurations. Read on.
- First way
By contacting JetPack Support , filling simple contact form and asking them to do so. They will in my experience respond in about 2-3 days.
You can as well submit post on one off these threads on WordPress forum. WordPress staff responds in few days to week or two.
This is easier and maybe only possible way for most of the people.
Now second way is bit more complicated and has some requirements.
- Second way
Essentially you will be installing new instance of WordPress under your domain that you want to remove and installing JetPack plugin. After that simply connect and disconnect your website and remove your new WordPress installation if needed.
This method is for people who cannot wait few days or weeks and want to do in instantly.
And before doing this please backup your whole website under domain that you want to remove, including all files and database! This is important if you lose or destroy something I am not responsible. I assume that you know basics of web administration and using webserver control panel (eg. cpanel) as well installing WordPress. If you don't know how to install it check their official 5-min guide.
This might be hard to do for some people especially those who already have new instances of websites running under domains that they want to be removed. In that case I recommend you ether use something like mailing list or social media (facebook, google+, twitter, etc. ) to notify your readers/viewers that you will be taking website for maintenance for about 15-20 min.
You will need to have access to yours domain DNS configuration as well as your web server.
First thing that you want is to change your domain DNS to new server DNS or if you are using same server (eg. Shared hosting, private server) you don't have to change anything about your domain DNS.
Create new folder and change Sites root to new folder. Care to not delete your old web site folder.
Now you need to install your WordPress installation under that new folder and domain that you want to remove. After installation install JetPack plugin and Connect to JetPack and click again to disconnect in JetPack plugin.
I understand that this is impossible for some people but as it is a possibility I wanted to post it.
Good luck and have a nice day.