My Setup is:

/home/account_name/domain/Joomla+JMS EXT

When the salve site is create with "Alias" through the template from the front-end, the "alias"
symbolic link is always getting created under the root directory where the joomla is installed.

i.e, /home/account_name/domain/Joomla+JMS EXT + alias symbolic link

We want to alias symbolic link to deploy directory to be created out side the root directory where the joomla is installed.

i.e, /home/account_name/wholesale/alias

How we can do it?

You can create alias anywhere as long as you have the permission to create the link in this directory.
You can also use the keywords to compute the location where to store the alias.

For example, you can set the alias = {home}/wholesale/{site_alias}
Verify the {home} value in your JMS settings.
It should be assigned to /home/account_name